However, yes, you can do this with pure mod_rewrite, too, e.g.:
RewriteRule ^Models/ - [F]
will send a FAIL code rather than ANY content from the Models subdirectory. Given that, the ONLY way for you to use any Models file is to include() it (or similar) via PHP code from a script in an open directory. I don’t know what you have in ANY of your subdirectories but Media may cause a problem if it contains your website’s images. Same with any of the other subdirectories.
Learn more about mod_rewrite by having a look at the tutorial Article linked in my signature (from years of answering the same questions in this forum).
[COLOR="Blue"]RewriteEngine on[/COLOR]
# RewriteCond %{REQUESTED_FILE} !^/?media/?$
# I don't know what {REQUESTED_FILE} is!
RewriteCond %{REQUEST_URI} !^/?media/?$
# Apache 1.x AND Apache 2.x
# NOT media as the start of something or a directory???
RewriteRule ^/?([a-zA-Z]+)/?$ http://127.0.0.1/crille/test/ [NC,L]
# the optional trailing slash can cause problems with relative links
# in the served script - remove it if it's there!
# WHY use localhost in the redirection?
# The No Case flag is only useful in matching
# case INsensitive strings, i.e, {HTTP_HOST}