mkv clusters to fmp4

I have an mkv file that I already parsed and extracted its content.
the content is basically spread over different clusters which in turn are subdivided into blocks, I'm already parsing all of this.
the result file I have is basically the mdat portion of an mp4 file, only the mdat.
I would like to transform these mdat to fmp4 files playable by MS. 

can this be done and how ? 
Thank you :) 