This technique can not only be used for new pads, but also to try to diagnose other problems you might be having with your current rotors.
On my motorcycle I have a slight warp in the left side rotor so it's not quite useable so I decided to go ahead and buy some used oversized rotors since I'm going to be there anyways. This technique can be applied to all rotors and I highly recommend it!!
After checking to make sure that your rotors are straight (I mounted mine in a lathe and used a runout gauge to check for both concentricity [how circular they are] and also to make sure that there was no warpage on the disk itself) go ahead and give them a good cleaning.
Now I do have two methods available to me, one of which can be done at the techshop and the other is more specailized so I'll be covering the one that most people will have access to which is going to be a standard drill cleaning method.
-Drill or Mill with circular vice (YAY TECHSHOP!!!)
-quiklok carrier (or similar)
-*Medium Grade metal surface prep disks (non-silicate and non abrasive)
*welding prep disks work very well, they leave no residue and they do not marr the rotors at all under normal useage. Fine grade will work as well and leave you with a slightly better surface finish but it will take quite a while to do so as it is very slow to remove the material.
Step 1: Initial clean
You can put painters tape over the orfices but I decided to just go ahead and unmount them completley from the rim.
Now that you're staring at your rotors you should notice some slight discoloration (brownish, grey) all over the rotors. This is what we're trying to remove.
As you can see in the picture below, In my case I have some really light surface rust from being next to steel parts (the rotors themselves are stainless steel) and just general dirt, and some brake pad reside (not good for new pads).
The first step in cleaning is a general degreasing using simple green or a similar environmentally friendly product to get off the major grease and grime. If you leave it on there it will be fine but you will load up your scouring pads very quickly and it will end up costing you quite a bit more in time, labor and more pads.