protecting flash drive when booting UBCD

Hi,

I am sorry if this question was asked and I was unable to locate the post it was asked in.

I have read stories where users indicated potential infection of thumb drives when used for booting a PC.

I wonder if anyone protects their UBCD flash drive (thumb drive, memory stick). And, if you do, how do you protect the flash drive when using it on a possibly infected computer?

Thank you.