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Initial actions: I wanted to copy some files that were very close in total size to the USB stick memory size (<8G). So I checked size of all files vs available space. A few more KB were needed for everything to fit, so I checked if the drive is completely blank.

Problem: But when I checked the USB stick, it had 67MB used space, although it was completely empty (as in no hidden files or partitions). Formatting it while monitoring space usage with my own software, reveled that while formatting it NTFS via windows explorer, the system it does allocate all space and after a few mili-seconds a temporary file appears and disappears removing 67MB from the drive's space. (7.48 became 7.41GB available).

System info: Win 7 x32 running on notebook, no viruses, no antviruses, no 3rd party programs installed (just blank OS).

Fix: What I did to have all space: I switched from DevMng to optimize for performance and reformatted to FAT32, 64k cluster size. That made the 67MB of windows spy-stuff gone and showed me an allocated space of only 64kb. The difference was enough for my files to be fit and copied in one run.

So can anyone tell me what was that 67MB of system-hidden space ?

Thank you for your answers but, as I mentioned initially, there is no hidden anything on the drive; no System information, no recycler or any type of file/folder, fake ones included (the new pseudo-folders W7 uses). I check this independently of windows and explorer, with personal FM that shows everything in a file structure, including the unseen even if 'show hidden' is on.

The space is somehow allocated outside the file system, probably directly into the allocation table.

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    I can't take this as a serious question. I really...really tried. Between the name you choose to use, it can't be done, this seriously can't be serious. There wasn't a "secret spy partition" on your drive
    – Ramhound
    Commented Jan 23, 2015 at 11:58
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    It was NTFS, so it wouldnt be completly empty, there would be a $logfile , $bitmap MFT and MFTmirror and possibly $jrnl file items. Use a disk editor, cluster analiser, or something like mydefrag (free defragger not to defrag but because of the good displayng of the clusters and contents) to view all the items that exist in the clusters. see the file systems file items. Fat and Fat32 have a different layout than a NTFS formatting would have. –
    – Psycogeek
    Commented Jan 23, 2015 at 13:16

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Windows versions since XP have created a "System Volume Information" folder on all partitions formatted with Windows. As far as I know, however, there's nothing critical in this folder, since Windows can happily read and write partitions created with other software that don't contain it. It'll have a minimum size of one cluster -- which is close to the "missing" space you were seeing.

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When you plug in a flash drive into Windows it temporarily copy's over a ready boost; to test the flash drive, but this does not explain the size. When you add then delete data on a USB flash drive it writes it to zeros, and just like Windows when you empty the recycle bin it's still there waiting to be written over. sometimes a USB will create a hidden folder called "tmp" or something like: ~root/trash0 I believe and it stores deleted data that sometimes cannot be seen; even if folder view is set to show hidden. Windows in general has a hard time reading everything. I learned this while creating a persistence live USB. you can partition a 20 gig USB and Windows may read it as like a 10 gig flash drive, so to check what Windows explorer cannot I suggest using Gparted and if you have no luck wiping everything you could always to a quick erase with DBAN )Deriks Boot and Nuke)

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