Generally all Pen-Drive or Flash Disk run in FAT 32 format System. also Flash Disk Format in FAT format. But if wish to use NTFS Format, of course should be Use. for NTFS format, at first click on the right button, then go properties / hardware option & select the current Pen Drive or Flash Disk, then from Properties\Policies, select Optimize for Performance, Then Click Ok.
Then the Pen Drive or Flash drive Use The NTFS System.
Note :: before do the format of Flash Disk or Pen drive, must remove Your important data, otherwise data are corrupted or delete.