I've talked about some different things:

The 1st one is explained by JVene. You could use OS services.
By the way, I have a question to JVene: Are you sure about XP and Vista? It seems, XP has some improvement in it's security system( NTFS5 vs NTFS4 on Win2K).

To Igeru: what encryption algorithm are you using? I've read some of your older threads and pointed that you read your file byte after byte. It seems to be not the best method, read file by larger chunks and naturally use a standard cipher. Look at some publicly available encryption algorithms. Also have a look at this: http://www.cryptopp.com/

If you're implementing a kind of Caesar's cipher, it still would be better to use an OS services.

The 2nd is the following:

You are going to store some data in encrypted file. How are you going to use it? Are you going to store some settings there or you are writing a scrambling utility for user's files?