When it comes to a tool that can handle any kind of media manipulation, you quickly think of the open-source FFmpeg tool. And indeed FFmpeg can encode, and encapsulate all different media file types not to mention perform a large number of media manipulations. But if you want to work with MP4 files and do not really want to re-encode the files, then you can use the free tool MP4Box.
MP4Box is a multimedia package that offers a surplus of features when modifying multimedia files. Just like FFmpeg, it is also a command line interface (CLI) tool and gives a number of command line options using which you can convert multimedia files, import different video formats, merge and split audio and video streams, and even attach external subtitles. MP4Box is a part of the GPAC open-source multimedia project which is intended for performing many manipulations on multimedia files like AVI, MPG, TS, but mostly on ISO media files (e.g. MP4, 3GP).
Since it is a command line interface tool, many people might find it a little hard to use. For those people, there are a number of GUI front-end applications available. For example, YAMB (Yet Another MP4Box) is a very capable front-end for the Mp4Box tool. YAMB comes with all the tools in the package including MP4Box itself. But the version of MP4Box included in YAMB package is older version. You can easily point YAMB to the latest version of MP4Box located somewhere else on your hard drive.
From the YAMB GUI, you can create a new MP4 file containing video streams, audio streams and subtitles. You can edit media files to split and join them, to extract video stream, to extract audio stream, to convert the subtitle formats, to add or remove META tags from MP4 files.
MP4Box together with YAMB can be a really powerful tool to modify and create MP4 and 3GP files. It is not as comprehensive as FFmpeg, but it is really fast.
You can download MP4Box from https://gpac.wp.imt.fr/mp4box/.