diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 2275ab41c..28c273917 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -60,8 +60,8 @@ Example:
 #include "RobotInterface.h"
 #include "Signal.h"
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/SpatialMomentum.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/SpatialMomentum.h>
 #include <iDynTree/KinDynComputations.h>
 
 #include <ostream>
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 10e25bd8e..4253a96b2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,7 +2,7 @@
 # This software may be modified and distributed under the terms of the
 # GNU Lesser General Public License v2.1 or any later version.
 
-cmake_minimum_required(VERSION 3.5)
+cmake_minimum_required(VERSION 3.16)
 project(WB-Toolbox LANGUAGES CXX VERSION 6.0.0)
 
 if(WBT_BUILD_DOCS)
diff --git a/toolbox/base/CMakeLists.txt b/toolbox/base/CMakeLists.txt
index 8eb4c15b2..4376f1d8f 100644
--- a/toolbox/base/CMakeLists.txt
+++ b/toolbox/base/CMakeLists.txt
@@ -24,7 +24,7 @@ target_link_libraries(WBToolboxBase
     YARP::YARP_init
     YARP::YARP_dev
     iDynTree::idyntree-model
-    iDynTree::idyntree-modelio-urdf
+    iDynTree::idyntree-modelio
     iDynTree::idyntree-high-level)
 
 target_include_directories(WBToolboxBase PUBLIC
diff --git a/toolbox/base/src/RobotInterface.cpp b/toolbox/base/src/RobotInterface.cpp
index f514ce82e..db995066a 100644
--- a/toolbox/base/src/RobotInterface.cpp
+++ b/toolbox/base/src/RobotInterface.cpp
@@ -11,10 +11,10 @@
 
 #include <BlockFactory/Core/Log.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingMatrices.h>
-#include <iDynTree/Model/Indices.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingMatrices.h>
+#include <iDynTree/Indices.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelLoader.h>
 #include <yarp/dev/ControlBoardInterfaces.h>
 #include <yarp/dev/PolyDriver.h>
 #include <yarp/os/Bottle.h>
diff --git a/toolbox/base/src/WBBlock.cpp b/toolbox/base/src/WBBlock.cpp
index 9c9c55f7a..bccc1d0b6 100644
--- a/toolbox/base/src/WBBlock.cpp
+++ b/toolbox/base/src/WBBlock.cpp
@@ -16,11 +16,11 @@
 #include <BlockFactory/Core/Parameter.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/Transform.h>
-#include <iDynTree/Core/Twist.h>
-#include <iDynTree/Core/VectorDynSize.h>
-#include <iDynTree/Core/VectorFixSize.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Transform.h>
+#include <iDynTree/Twist.h>
+#include <iDynTree/VectorDynSize.h>
+#include <iDynTree/VectorFixSize.h>
 #include <iDynTree/KinDynComputations.h>
 
 #include <array>
diff --git a/toolbox/library/CMakeLists.txt b/toolbox/library/CMakeLists.txt
index aeba0b852..d0784adf8 100644
--- a/toolbox/library/CMakeLists.txt
+++ b/toolbox/library/CMakeLists.txt
@@ -101,7 +101,7 @@ list(APPEND WBTOOLBOXLIBRARY_EXT_LIBRARIES
     YARP::YARP_math
     iDynTree::idyntree-core
     iDynTree::idyntree-model
-    iDynTree::idyntree-modelio-urdf
+    iDynTree::idyntree-modelio
     iDynTree::idyntree-high-level)
 
 # Additional dependency of the SimulatorSynchronizer block
diff --git a/toolbox/library/src/CentroidalMomentum.cpp b/toolbox/library/src/CentroidalMomentum.cpp
index 36bd0dcd3..a7bcf9929 100644
--- a/toolbox/library/src/CentroidalMomentum.cpp
+++ b/toolbox/library/src/CentroidalMomentum.cpp
@@ -13,8 +13,8 @@
 #include <BlockFactory/Core/BlockInformation.h>
 #include <BlockFactory/Core/Log.h>
 #include <BlockFactory/Core/Signal.h>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/SpatialMomentum.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/SpatialMomentum.h>
 #include <iDynTree/KinDynComputations.h>
 
 #include <ostream>
diff --git a/toolbox/library/src/CentroidalTotalMomentumMatrix.cpp b/toolbox/library/src/CentroidalTotalMomentumMatrix.cpp
index 41eccf660..bd90368e5 100644
--- a/toolbox/library/src/CentroidalTotalMomentumMatrix.cpp
+++ b/toolbox/library/src/CentroidalTotalMomentumMatrix.cpp
@@ -16,11 +16,11 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixDynSize.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixDynSize.h>
+#include <iDynTree/Transform.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <memory>
 #include <ostream>
diff --git a/toolbox/library/src/DotJNu.cpp b/toolbox/library/src/DotJNu.cpp
index 1a4980c41..0be4bddea 100644
--- a/toolbox/library/src/DotJNu.cpp
+++ b/toolbox/library/src/DotJNu.cpp
@@ -15,10 +15,10 @@
 #include <BlockFactory/Core/Parameter.h>
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/VectorFixSize.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/VectorFixSize.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <memory>
 #include <ostream>
diff --git a/toolbox/library/src/ForwardKinematics.cpp b/toolbox/library/src/ForwardKinematics.cpp
index aa9365fb0..796eb8819 100644
--- a/toolbox/library/src/ForwardKinematics.cpp
+++ b/toolbox/library/src/ForwardKinematics.cpp
@@ -16,10 +16,10 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Transform.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <ostream>
 #include <tuple>
diff --git a/toolbox/library/src/GetLimits.cpp b/toolbox/library/src/GetLimits.cpp
index 72a26ff68..50f44ed4f 100644
--- a/toolbox/library/src/GetLimits.cpp
+++ b/toolbox/library/src/GetLimits.cpp
@@ -16,9 +16,9 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/IJoint.h>
-#include <iDynTree/Model/Indices.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/IJoint.h>
+#include <iDynTree/Indices.h>
+#include <iDynTree/Model.h>
 #include <yarp/dev/ControlBoardInterfaces.h>
 
 #include <cmath>
diff --git a/toolbox/library/src/InverseDynamics.cpp b/toolbox/library/src/InverseDynamics.cpp
index 2d2cc80c4..d7ee2221e 100644
--- a/toolbox/library/src/InverseDynamics.cpp
+++ b/toolbox/library/src/InverseDynamics.cpp
@@ -14,14 +14,14 @@
 #include <BlockFactory/Core/Log.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/VectorDynSize.h>
-#include <iDynTree/Core/VectorFixSize.h>
-#include <iDynTree/Core/Wrench.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/VectorDynSize.h>
+#include <iDynTree/VectorFixSize.h>
+#include <iDynTree/Wrench.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/JointState.h>
-#include <iDynTree/Model/LinkState.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/JointState.h>
+#include <iDynTree/LinkState.h>
 
 #include <memory>
 #include <ostream>
diff --git a/toolbox/library/src/InverseKinematics.cpp b/toolbox/library/src/InverseKinematics.cpp
index 661a06900..4ad5c0d9d 100644
--- a/toolbox/library/src/InverseKinematics.cpp
+++ b/toolbox/library/src/InverseKinematics.cpp
@@ -7,8 +7,8 @@
 #include <Eigen/Core>
 #include <iCub/iKin/iKinFwd.h>
 #include <iCub/iKin/iKinIpOpt.h>
-#include <iDynTree/Model/DenavitHartenberg.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/DenavitHartenberg.h>
+#include <iDynTree/ModelLoader.h>
 #include <iDynTree/iKinConversions.h>
 #include <wbi/wholeBodyInterface.h>
 #include <yarp/os/ResourceFinder.h>
diff --git a/toolbox/library/src/Jacobian.cpp b/toolbox/library/src/Jacobian.cpp
index d9526e8af..4bca9a15c 100644
--- a/toolbox/library/src/Jacobian.cpp
+++ b/toolbox/library/src/Jacobian.cpp
@@ -16,11 +16,11 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixDynSize.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixDynSize.h>
+#include <iDynTree/Transform.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <memory>
 #include <ostream>
diff --git a/toolbox/library/src/MassMatrix.cpp b/toolbox/library/src/MassMatrix.cpp
index 3e48f1ceb..a9472cfae 100644
--- a/toolbox/library/src/MassMatrix.cpp
+++ b/toolbox/library/src/MassMatrix.cpp
@@ -14,8 +14,8 @@
 #include <BlockFactory/Core/Log.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixDynSize.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixDynSize.h>
 #include <iDynTree/KinDynComputations.h>
 
 #include <ostream>
diff --git a/toolbox/library/src/RelativeJacobian.cpp b/toolbox/library/src/RelativeJacobian.cpp
index a2d5463ca..5e52a7167 100644
--- a/toolbox/library/src/RelativeJacobian.cpp
+++ b/toolbox/library/src/RelativeJacobian.cpp
@@ -16,11 +16,11 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixDynSize.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixDynSize.h>
+#include <iDynTree/Transform.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <memory>
 #include <ostream>
diff --git a/toolbox/library/src/RelativeTransform.cpp b/toolbox/library/src/RelativeTransform.cpp
index e7e2c0947..fefca0420 100644
--- a/toolbox/library/src/RelativeTransform.cpp
+++ b/toolbox/library/src/RelativeTransform.cpp
@@ -16,10 +16,10 @@
 #include <BlockFactory/Core/Parameters.h>
 #include <BlockFactory/Core/Signal.h>
 #include <Eigen/Core>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Transform.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 #include <ostream>