If you've had your intercooler for awhile, it probably looks like this:

I've tried a few things to straighten those fins out like thin files, knives, paperclips, etc. and then I tried tweezers. Those worked the best hands down.
Grab a pair of tweezers, a can of compressed air, and a toothpick or paperclip.

Straighten out each fin like this: insert the tweezers on either side of it, squeeze, and pull the tweezers out, here's a diagram:

Some of your fins my be creased very badly. For those just try to pull the crease out first, then straighten it.
Be careful not to squeeze too hard, because if the fin was damaged by whatever creased it, you can rip it apart. You'll know what too hard is because you can feel the thin aluminum "stretching".
Just TAKE YOUR TIME, and do a good job. There's no sense rushing. It took an hour and 40 minutes to do the whole intercooler.
The toothpick is for the inevitability of tiny rocks that make their way between the fins and get stuck.
The compressed air is for the rocks that are too stubborn and may blow out the other side.
Here's what my intercooler looked like after: