In the past years, algorithms for 3D shape tracking using radial functions in spherical coordinates represented with different methods have been proposed. However, we have seen that mainly measurements from the lateral surface of the target can be expected in a lot of dynamic scenarios leading to an error-prone shape estimate in the top and bottom parts of the target when using a representation in spherical coordinates. We, therefore, propose to represent the shape of the target using a radial function in cylindrical coordinates, as this only represents regions of the lateral surface, and no information from the top or bottom parts is needed. In this paper, we use a Fourier-Chebyshev double series for 3D shape representation since a mixture of Fourier and Chebyshev series is a suitable basis for expanding a radial function in cylindrical coordinates. We investigated the method in a simulated and real-world maritime scenario with a CAD model of the target boat as a reference. We have found that shape representation in cylindrical coordinates has decisive advantages compared to a shape representation in spherical coordinates and should preferably be used if no prior knowledge of the measurement distribution on the surface of the target is available.