I want to store some important data on my USB flash drive. Data should be in an encrypted format and the data should be retained on the USB drive even if the USB flash drive is formatted. Is there any software to do this? I want to do this only on Windows.
You can use Fbinst to create a hidden partition (tutorial), which should resist formatting. To encrypt the partition, you can use TrueCrypt. I don't know of any free software which does both; it's most likely a two-step process: create the hidden partition, then encrypt it.
If you do decide to use Fbinst, you can download a version with an English GUI from this link.