Are the file types restrictive?

I'm new to digital cameras and photography in general and recently i have been reading a lot of specs which for the most part i can understand, but I see a lot of Compact Flash cards saying that they are formatted in FAT, which from a computer point of view means that I cannot transfer my photos from the camera which are in FAT format to my computer which is in NTFS format and likely the Windows Vista format (I forgot what it's called). Though this may not be true when dealing with cameras so can someone tell me will the files on a FAT formatted CF Card work on a NTFS formatted hard drive?

*nods* it's been a bit since I delt with this, but im 99% sure that NTFS can deal with FAT formatted files.

I can reassure you that extra 1%, there is no problem what-so-ever with FAT files on an NTFS system.