The modeling and simulation of cylindrical surfaces with consideration of form defects have led to considerable research outcomes in the field of Computer-Aided Tolerancing (CAT). However, further consideration of surface deformations caused by external forces still remains a challenge. To address this issue, this paper properly considers the form defects and surface deformations for tolerance analysis of cylindrical components. First, form defects are considered by modeling skin model shapes of cylindrical surfaces. Afterwards, the tight fit and loose fit of a pair of cylindrical surfaces are identified, and the simulation methods of their positioning are presented. Specifically, for tight fit situation, a k-d tree based Iterative Closest Point (ICP) algorithm is used, and for loose fit situation, the constrained registration approach is adopted. Moreover, a Conjugate Gradient-Fast Fourier Transform (CG-FFT) method is presented for the consideration of surface deformations. In addition, simulations of given examples are conducted, which show the considerable effects of form defects and surface deformations. The simulations may also help determine the best performance of the to-be-assembled cylindrical components.