Initializing USB flash drive

Windows

You can run Command Prompt as administrator.

Notes: FAT32/exFAT file systems are recommended for USB flash drives.
The FAT32 supports max 32GiB volume size and max 4GiB file size.
The exFAT supports over 32GiB volume size but it doesn’t work on Windows XP (need additional driver).

Linux

First, remove partition table on your USB flash drive.
sudo dd if=/dev/zero bs=512 count=4096 of=/dev/${USB_FLASH_DRIVE}
The ${USB_FLASH_DRIVE} must be a device name like sdx, not a partition name like sdx1.
Warning: If you write local storage (ex: hdd/ssd) name on it by mistake, you will lose data on the local storage so please check the name carefully by lsblk.

Then you can make a new partition table, partition, and file system by your preferred tools. (ex: Gparted, parted, fdisk, gdisk, mkfs.fat, etc)