Care should be taken to ensure that any bootable floppies have been checked for the presence of boot sector viruses and these disks should be write-protected to ensure no future infection takes place.
Even non-bootable disks can spread a boot sector infection when they are accessed. Further, a boot sector infected hard drive will also infect any floppies used in the system. Where applicable, use write-protected floppies to protect against this.
To write-protect a floppy disk, hold it so that the metal plate is facing downwards. Along the top edge there may be an open square. Look closely and you will find a small cover that can be pushed back and forth over the open square. If the cover is closed, i.e. the square is covered, the disk can be written to. If the cover is open, i.e. the square is not covered, the disk cannot be written to and is considered write-protected.
Of course, you would not want to write-protect floppies you use to copy files to, as you would receive a write protection error the next time you attempted the copy.
Most of todays PCs no longer seek out the floppy drive during bootup, instead using the CD-ROM drive as the first boot device. This can be configured via the system CMOS screen to change the boot sequence to check the hard drive first, the CD-ROM drive second, and the floppy drive third, if at all.
Changing settings in CMOS incorrectly can result in system failure and should not be attempted by inexperienced users. Instructions for accessing the CMOS configuration screen for your PC can generally be found in the motherboard manual.
The first boot sector virus was discovered in 1986. Dubbed Brain, the virus originated in Pakistan and operated in full-stealth mode, infecting 360Kb floppies.
Perhaps the most infamous of this class of viruses was the Michelangelo virus discovered in March 1991. Michelangelo was a MBR and boot sector infector with a March 6th payload overwriting critical drive sectors. Michelangelo was the first virus to attract a large amount of media focus.
For more on this topic, see Boot sector/MBR virus resources