A container format processing tool performs syntax-aware manipulation of hierarchically organized syntax elements defined according to a container format in a media file. For example, a container format verifier checks conformance of a media file to a container format, which can help ensure interoperability between diverse sources of media content and playback equipment. Conformance verification can include verification of individual syntax elements, cross-verification, verification that any mandatory syntax elements are present and/or verification of synchronization. Or, a container format “fuzzer” simulates corruption of a media file, which can help test the resilience of playback equipment to errors in the media files. The container format fuzzer can simulate random bit flipping errors, an audio recording failure or incorrect termination of recording. Or, a container format editor can otherwise edit the media file in the container format.