There's a line in mods/_standard/file_storag/index.php that looks like the following that you can comment out to remove MyFiles.
[php]
<option value="2" <?php if ($owner_type == WORKSPACE_PERSONAL) { echo 'selected="selected"'; } ?>><?php echo _AT('my_files'); ?></option>
[/php]
You can find the files in content/file_storage/. Logged into the server's command prompt, you can run a command like "du -h" to show what space is being used, looking for the folders using excessive space. If you need to identify specific files, you'd match up the file id in the file_storage subfolders, with those listed in the "files" table in the database.