Considering the growing population and limited land availability, towering buildings with several basements have been built to increase floor area ratios while also meeting storage and parking needs. The design of Combined Pile Raft Foundations (CPRF) is crucial in supporting complex structures. Still, traditional techniques frequently ignore the interplay between pile-to-pile and pile-to-raft, compromising the overall performance and reliability of the foundation system. CPRF analysis is carried out using a variety of software packages, including PLAXIS 3D, SAP 2000, ETABS, and the recently announced ELPLA, each having its own set of capabilities, constraints, and user interfaces. To assess their reliability and applicability, this study offers a thorough comparative analysis of CPRF systems utilizing these techniques in five case studies. The findings indicate that PLAXIS 3D, a Finite Element Method (FEM) program, is the most accurate and dependable instrument for comprehensive analysis. In contrast, ELPLA was shown to underestimate loads, potentially leading to unsafe designs, whereas the Winkler Model for Piled Raft (WMPR) produced contradictory results, rendering both only appropriate for exploratory studies. These findings provide useful information for selecting appropriate software for CPRF analysis based on accuracy, dependability, and design safety factors.