I would like to ask if I install 64-bit program into Program Files (x86), will it still work as 64-bit?
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Yes. A 64 bit application will always only run 64bit, no matter where it's installed.
However, this will be a non-standard install location for a 64bit program, so would not be something I'd recommend. 64 bit applications should typically be installed to Program Files
, not Program Files (x86)
.

Reed Copsey
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Thanks, I just wanted to not have mess in applications installed. I wasn't used to install to default folders in Vista... – user1684488 Sep 19 '12 at 23:44