Methods, systems, and computer program products for software identification, dependency analysis, and manipulation of file system layers of container images are provided herein. A computer-implemented method includes extracting multiple layer files from an input image; identifying software components in each of the extracted layer files; manipulating the input image based on said identifying and user-defined parameters, wherein said manipulating comprises (i) selecting a sub-set of the layer files for retention, (ii) removing a sub-set of the layer files, and (iii) modifying one or more of the layer files selected for retention and/or inserting one or more new layer files in place of one or more of the removed layer files; and outputting a modified version of the input image that includes the sub-set of the multiple layer files selected for retention and any new layer files inserted in place of removed layer files.