Many people don't realise it, but running WITHOUT shoes can give you blisters too. Not the normal shoe and sock rubbing against flesh type, but rather the flesh rubbing against tar/dirt type.
At the moment, my current barefoot mileage is in the region of 10km a week, on paving/tar, broken up into 3 sessions of just over 3km each. This is just long enough for me to enjoy the freedom of running barefoot and feel when I'm doing things wrong. This is also long enough to acclimatise my feet to the rougher compounds with only a minimal amount of damage on each run.
Unfortunately, sometimes I'm a little over-eager or tired and I either run too far, too fast, or with appalling form (ie too much toeing-off) and as a result I end up with a blister on one of my toes - normally the one just next to the little toe for some reason.
Anyway, my blister treatment follows, but first a warning:
If you're a barefoot runner, or interested in running barefoot (hence you're reading this) this isn't likely to be you, but it may just be your other half/mother/GP etc, so best not perform this in front of them or let them know about this. I know my wife gets very squeamish so I have to do this when she's not about.
Right, now we've got that out of the way, we can get down to the nitty gritty...
That's it. You're done.
Things will be a little sensitive for the first few hours, but you'll soon forget about it. Within a couple of days, you should find your blister will have healed, without any loss of skin and the thread will have worked it's way out all by itself. You may even find you can run on it within 24 hours, so your training shouldn't be affected too much.
I'm really not sure where I first heard this, but ever since trying it many many years ago as a kid, I've stuck with it. I don't know of a more effective and quicker treatment for blisters.