Method of operating an orthopedic surgery planning system, comprising the steps of: - importing at least one medical image into a computer system; - 3D model generating of at least one anatomical structure selected, based on the at least one medical image and on a value or a set of density values of the at least one anatomical structure, using an extraction of a polygonal mesh of an isosurface from a three-dimensional scalar field called voxels, said anatomical structure 3D model being a matricial volumetric image composed of arrays of voxels; - segmenting the anatomical structure 3D model according to the value or set of density values previously selected; - Accessing a 3D prosthetic material model database to select at least one prosthetic material 3D model, said 3D model being a vectorial image comprising a set of geometric representations; - Combining models originated from structurally different images, by intersecting the 3D models representing the at least one prosthetic material and the at least one anatomical structure selected in a user interface of the computer system; said method being characterized in that it further comprises the step of - interacting in the user interface with the created 3D models of the anatomical structure and the prosthetic material, in a 2D environment area and in a 3D environment area; said 3D models being updated in real time in both 2D and 3D environments areas; the 2D environment area comprising three 2D plans: axial, coronal and sagittal; - Inserting at least one different anatomical structure to the 3D model representation of the at least one anatomical structure selected by segmenting said anatomical structure 3D model according to a value or a set of density values; - Simulating the implantation of a prosthetic material in said anatomical structure 3D model; - Evaluating the most suitable prosthetic material, by assessing the impact that the current planning might have on the surrounding structure(s) predicting possible complications that may arise after the surgery; - Generating a report by the computer system with information about the planning performed which can be saved in a memory. - importing at least one medical image into a computer system; - 3D model generating of at least one anatomical structure selected, based on the at least one medical image and on a value or a set of density values of the at least one anatomical structure, using an extraction of a polygonal mesh of an isosurface from a three-dimensional scalar field called voxels, said anatomical structure 3D model being a matricial volumetric image composed of arrays of voxels; - segmenting the anatomical structure 3D model according to the value or set of density values previously selected; - Accessing a 3D prosthetic material model database to select at least one prosthetic material 3D model, said 3D model being a vectorial image comprising a set of geometric representations; - Combining models originated from structurally different images, by intersecting the 3D models representing the at least one prosthetic material and the at least one anatomical structure selected in a user interface of the computer system; said method being characterized in that it further comprises the step of - interacting in the user interface with the created 3D models of the anatomical structure and the prosthetic material, in a 2D environment area and in a 3D environment area; said 3D models being updated in real time in both 2D and 3D environments areas; the 2D environment area comprising three 2D plans: axial, coronal and sagittal; - Inserting at least one different anatomical structure to the 3D model representation of the at least one anatomical structure selected by segmenting said anatomical structure 3D model according to a value or a set of density values; - Simulating the implantation of a prosthetic material in said anatomical structure 3D model; - Evaluating the most suitable prosthetic material, by assessing the impact that the current planning might have on the surrounding structure(s) predicting possible complications that may arise after the surgery; - Generating a report by the computer system with information about the planning performed which can be saved in a memory.