I think the problem is that you are calling a function from the base workspace then expecting the variables created in the function to exist in the base workspace? If that is so, you need to understand that functions have their own workspaces. Any variables you need from a function should be passed out or saved from within the function for later loading at the command line.
For example, at the end of the function, put this line:
save myfuncvars
Then from the command line:
load myfuncvars
Now all of the variables in the function are in your base workspace. Be aware that any pre-existing variables which have the same names as a variable in the function will be lost. Thus to be safe, do this at the command line:
MFV = load('myfuncvars');
Then MFV will be a struct containing the function variables as fieldnames.
