You could make your DIRs unaccessible from WINDOWS.
But before doing this, you should know the basics of DOS.

DOS COMMANDS

REN Rename syntax: [REN Hello.txt Hi.txt] renames Hello.txt to Hi.txt

The process is to rename your filename as an unknown character in WINDOWS.
Because some characters in DOS, doesn't display in WINDOWS.
You can rename your filename or even just add an unknow character.

TO MAKE UNACCESSIBLE
1) You have to go to Command Prompt [run COMMAND.COM]
2) Go to the desired DIRECTORY/FOLDER
3) Type in "REN filename.txt filename .txt [rename the filename with an
unknown character, the ASCII, alt+255]
the unknown character alt+255 is only an empty
character that is not accessible in WINDOWS
4) After doing so, type "EXIT" to exit DOS, and return to WINDOWS.
5) Finish...

TO REGAIN ACCESS
1) Just use your common sense [refer to "TO MAKE UNACCESSIBLE"]
2) Rename [filename w/ alt+255] to filename.txt