Looking inside the intercooler of my '06 MINI Cooper S when I had it off recently, to replace the supercharger, I noticed that the inside was coated in a thin film of oil. This decreases the efficiency of the intercooler by fouling up the heat transfer between the intercooler fins and the air flowing through it.This is the solution I came up with.

Disclaimer: I don't know how your intercooling system works. This How To won't do damage to a first generation MINI Cooper if followed properly but there could be a slight difference in your system that could cause problems. It's unlikely but possible so read the Instructable and then make a decision based on your situation. It is also possible that the inside of your intercooler may never need cleaned. In Gen 1 MINI's the crankcase vents into the air system, which means oil vapor and mist gets into the air system, making a mess of things.

Step 1: Materials and Tools

Materials

Acetone, 1 qt, $7 - Acetone evaporates quickly and is safe for the materials we will be using it on.
Rubber Bands, x 2, Free - Look at the size of the openings on your intercooler and choose your bands accordingly. Heavy duty bands are best.
Plastic Bags, x 2, Free - Try to find two without holes.

Tools

Gloves - Make sure solvent won't dissolve them or soak through.
Mask - Brain cells are good, acetone hates brain cells.
Bucket - I used an oil pan already half full of junk coolent. Check all applicable local laws for disposal of used solvents.

Step 2: Prep and Safety

First you've got to get the intercooler out. I won't cover that here as every cooling system is different. Get a Chilton or Bently repair manual or use google. What I can say is that a lot of systems have rubber/plastic fittings on both in-flow and out-flow, remove these before continuing. If they need cleaned find something, a household cleaner like Simple Green, that doesn't have the potential to damage them.

Now that you have the intercooler out it's time to get ready to clean. Go to a well ventilated area (outside) and get everything together. Now suit up! Ok, just gloves and a mask, and safety goggles if you plan on getting really crazy and flinging acetone all over the place.

Step 3: Seal the Unit

Now we need to seal one end of the unit so you can put the acetone in without it running straight out and killing all the fish.
Stand the intercooler up on one end. Grab one of the plastic bags and spread it flat, it should be 2 layers thick everywhere. Now fold it at least once, depending on the size of the opening to be sealed. The sealing area needs to not only be as big as the opening but hang over the edge enough for the the rubber band to hold it. Which is the next step. Place the folded bag on the opening and stretch the rubber band around it. Be careful of making wrinkles in the plastic underneath the band, pull out any wrinkles that form.
Before moving on, fold the second bag so you are ready to seal the other end.

Step 4: Clean

Set the intercooler on the bottom of the bucket, open end up, and pour in the acetone, liberally. I used about 1/2 quart at first. Quickly seal the open end with the bag you already folded. Now pick the intercooler up and tilt it every which way, letting the acetone run side-to-side, top-to-bottom. You can shake the unit gently, just don't blow out your seals. Always keep as much of the unit over your bucket as possible while you do this.
After a couple of minutes of sloshing the solvent around, your seals will probably start to leak. At this point, or whenever you think you've cleaned long enough, with the unit over the bucket carefully remove whichever seal is leaking the worst and pour the used acetone into the bucket. You know it's been working because it goes in clear and comes out a sickly brown.
If the solvent you poured out was really dirty then pour a couple more splashes in and rinse it. I ended up rinsing mine 4-5 more times because it was so dirty. There is no need to re-seal the open end at this point if you are careful.

Step 5: Dry and Motor

Once you're done rinsing take the last seal off and shake out as many drips as you can. Place the unit outside somewhere it won't get dirty and let it dry for 10-20 min. At this point I cleaned the intercooler input pipe using the same method since I already had it off.
Acetone evaporates pretty quickly but I might wait 12+ hours to put the unit back on since there are lots of little places for it to hide and I'm sure it isn't great for a engine. If you have compressed air, blowing it through will reduce the dry out time.
Once you're sure it's dry, reinstall and enjoy the, probably imperceptible, performance gain of cooler intake air.
Remember to properly dispose of the waste acetone and keep on Motoring!