I wouldn't even bother with excluding the index.htm files located in your subdirectories via the robots.txt file.
Just use the following Meta tags in each document and you'll be good to go.
Code:
<META NAME="ROBOTS" CONTENT="NOINDEX,NOFOLLOW">
<META HTTP-EQUIV="CACHE-CONTROL" CONTENT="NO-CACHE">
<META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE">
<META NAME="ROBOTS" CONTENT="NONE">
<META NAME="ROBOTS" CONTENT="NOARCHIVE">
<META NAME="GOOGLEBOT" CONTENT="NOARCHIVE">