Quick primer: MKV is a container format that holds data like video, audio, and subtitles. MP4 is also a container format that is less advanced than MKV. MKV is superior than MP4 because it can hold more types of audiovisual data.
You shouldn't "convert" MKV to MP4 unless you're going to use a device that won't play back MKV; however all it takes is demuxing (removing) the streams from the MKV, then muxing (inserting) those same streams into a MP4 container. This is best if the MKV file has some form of MPEG-4 video (e.g. XviD, DivX, H.264) and MP3 audio.
One type of program that mux/demux MKV is MKV Merge.