We construct the 3D models of phytoplankton. In presented article we solve the problem about deformation of the created models: How to deform the model so that its shape should conform to the shape of the natural microorganism? We use the Free Form Deformation (FFD) for the solving of this problem. In the first case, when the dimensions of the microorganism are given, the distances between control points of the FFD are equated to these dimensions. In the second case, when a scientist has the image of the microorganism, he should deform the model, displacing the control points, so that the image edge and the model’s outer border has coincided. The control points location is used in the studying morphological changes of microorganisms and describing their shapes.