As mentioned best to start with a scale wheel version of the loco, if you can't find that, or in your case a great deal on a 3R version, as long as the loco is a 3/2 conversion capable, which the SD60E's are... you can purchase the scale wheels from MTH or any MTH dealer. From there it's a simple replacement of the wheelsets just paying attention to orientation of each wheelset. Once that is done, you can switch the locomotive over to 2R and depending on your control system either DC, DCS or DCC you may end up throwing the control switch as well, for example to DCC if you use DCC like NCE or Digitrax or another DCC system. At this point you should have a working locomotive with scale wheels that can run on 2R track and be controlled by DC, DCS, or DCC.
The next thing you might want to consider is fixing the pilots and extending the handrails for a more prototypical look, which is one of the key benefits of purchasing the scale wheel version direct from MTH. Neither of which is super difficult but does require some patience. Many on the forum have performed these steps so lots of experience to draw upon to help get you going in the right direction if you decide to go down this path. Rich's link above is awesome especially for the SD60E. Rich goes to another level and moves the truck sideframes in closer to the wheels for an even better look, he often also fills in the gap above the trucks and the below the chassis underframe to make a great locomotive even better! Really awesome low angle views of these locomotives often challenging you to determine if it's the prototype or a model. 
