If you're writing script files, variables aren't deleted until you explicitly clear them or until the caller's workspace is destroyed. If you're running the scripts from the prompt in the Command Window they're running in the base workspace, which persists until you close MATLAB.
If you're writing function files, the function workspace (and its contents) are destroyed when the function exits after the output arguments have been returned to the caller. [It's a bit more complicated than that with persistent variables, nested functions, etc. but that statement is accurate enough for purposes of this discussion.]
So breaking your program into "bite sized chunks", extracting commonly used steps into functions, can help keep your workspaces organized.
