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Are there any software packages, that allow to selectively limit filesystem access for each application? Do they have significant impact on system performance?

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sandboxie does the job for me, at nearly unperceaveable performance costs. –  Lorenzo Von Matterhorn Apr 6 '13 at 12:00

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I haven't used it but Sandboxie may be what you are looking for. Sandboxie runs your programs in an isolated space which prevents them from making permanent changes to other programs and data in your computer.

Sandboxie handles writes by default and it looks there are options for controlling reads. From the FAQ:

It should be noted, however, that Sandboxie does not typically stop sandboxed programs from reading your sensitive data. However, by careful configuration of the ClosedFilePath and ClosedKeyPath settings, you can achieve this goal as well.

Using Sandboxie in combination with a good firewall may give you the isolation you want.

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It looks like Sandboxie intercepts writes, but does not prevent from reading a directory and sending contents via network –  Roffal Apr 6 '13 at 12:01
    
I have been using "windows firewall notify", to keep programs from calling home. It works "with" windows firewall, which is pretty ineffective in it's normal settings. A person can use it to set the firewall to normally Block Everything, then notify about everything talking. Due to the extensive use internally and externally of programs using network methods to communicate, it was a total pain to get everything under control. But it is there now, and working. So many things talking so few needing to. –  Psycogeek Apr 6 '13 at 12:24
    
@Roffal added some info from the Sandboxie FAQ about controlling reads. –  Brad Patton Apr 6 '13 at 13:34
    
@Psycogeek thanks. Added a line about firewalls. Network access wasn't called out in the original post but good info to add. –  Brad Patton Apr 6 '13 at 13:35

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