A scalable comparison structure and methodology is provided that is suitable for comparing select data content in hundreds or thousands of files in an efficient manner. Section delimiters are defined to identify the sections of the files within which the select data content is located, and sets of unique sections are identified based on the select data content within the section. Thereafter, comparisons and reports are based on these unique content sections. If multiple files include a common set of data, a single unique content section is used to represent these multiple files. File groups are optionally defined, and different sets of select data content can be compared based on these file groups. The result of the comparison is presented in multiple hierarchical forms, including an identification of which files are different from each other, and an identification of the differences among the unique content segments.