(1) Abdominal aortic aneurysm (AAA) biomechanics-based metrics often reported may be over/under-estimated by including non-aneurysmal regions in the analyses, which is typical, rather than isolating the dilated sac region. We demonstrate the utility of a novel sac-isolation algorithm by comparing peak/mean wall stress (PWS, MWS), with/without sac isolation, for AAA that were categorized as stable or unstable in 245 patient CT image sets. (2) 245 patient computed tomography images were collected, segmented, meshed, and had subsequent finite element analysis performed in preparation of our novel sac isolation technique. Sac isolation was initiated by rotating 3D surfaces incrementally, extracting 2D projections, curve fitting a Fourier series, and taking the local extrema as superior/inferior boundaries for the aneurysmal sac. The PWS/MWS were compared pairwise using the entire aneurysm and the isolated sac alone. (3) MWS, not PWS, was significantly different between the sac alone and the entire aneurysm. We found no statistically significant difference in wall stress measures between stable (n = 222) and unstable (n = 23) groups using the entire aneurysm. However, using sac-isolation, PWS (24.6 ± 7.06 vs. 20.5 ± 8.04 N/cm2; p = 0.003) and MWS (12.0 ± 3.63 vs. 10.5 ± 4.11 N/cm2; p = 0.022) were both significantly higher in unstable vs. stable groups. (4) Our results suggest that evaluating only the AAA sac can influence wall stress metrics and may reveal differences in stable and unstable groups of aneurysms that may not otherwise be detected when the entire aneurysm is used.