The aim of this study was to prepare a self-made mathematical algorithm for the estimation of risk of stent-graft migration with the use of data on abdominal aortic aneurysm (AAA) size and geometry of blood flow through aneurysm sac before or after stent-graft implantation. AngioCT data from 20 patients aged 50–60 years, before and after stent-graft placement in the AAA was analyzed. In order to estimate the risk of stent-graft migration for each patient we prepared an opposite spatial configuration of virtually reconstructed stent-graft with long body or short body. Thus, three groups of 3D geometries were analyzed: 20 geometries representing 3D models of aneurysm, 20 geometries representing 3D models of long body stent-grafts, and 20 geometries representing 3D models of short body stent-graft. The proposed self-made algorithm demonstrated its efficiency and usefulness in estimating wall shear stress (WSS) values. Comparison of the long or short type of stent-graft with AAA geometries allowed to analyze the implants’ spatial configuration. Our study indicated that short stent-graft, after placement in the AAA sac, generated lower drug forces compare to the long stent-graft. Each time shape factor was higher for short stent-graft compare to long stent-graft.