Port to NumPy.
(Joke.)
Usually in Matlab you have some files written as functions, and some as scripts. Scripts do things like load the data you want to process, and feed it to the functions, and graph it.
To organize things I would start at the top level script and find out which functions do the loading, graphing, processing, etc. Keep the scripts in a top level directory and try to separate the functions out into subdirectories, according to the purpose of the function. Put dependencies of a function into the same subdirectory. Try to make it so that no code in a directory depends on anything in a parent directory (or cousin directory).
Whenever you figure out what a function does and what its arguments are, write a doc comment.
This assumes the person who wrote the code was reasonable. If not, Matlab makes it easy to plunk everything down into one directory and have everything depend on everything else in a rickety tower of code, so you may end up doing a lot of refactoring.