There are two ways to do this; one of these ways has been present for quite a while, and I'm not sure if it was intentional. But recently, there have been changes to the Cutting Edge build which has allowed for more deliberate manipulation of this element.
However, this change is yet to arrive on the Stable build, so if you refuse to switch, then you'll have to settle for the gimmick method or wait until it arrives. If you don't know what these builds/release streams are, chances are that you're on the Stable build.
FOR STABLE BUILD USERS:
1) Go into the folder of the skin you wish to perform this on. 2) Locate two files "hitcircle.png" and "hitcircleoverlay.png." If they are followed by "@2x," use those instead. 3) Use any image editor that supports transparency (GIMP, SAI Paint Tool, Paint .net, Photoshop, etc. but not MS Paint) 4) Create a new, blank image. 5) Create two layers in this image. 6) Cut and paste the contents of "hitcircleoverlay.png" into the first layer. 7) Cut and paste the contents of "hitcircle.png" into the second layer. Both hitcircleoverlay.png and hitcircle.png should be blank. Save these two images as blank. 8) Merge the two layers and save the image as "hitcircleoverlay-0.png." If your images were originally followed by @2x, name the file "[email protected]." 9) Finally, check the skin.ini and make sure the option of "HitCircleOverlayAboveNumer" is set 1 and not 0 (yes, it's numer and not number, for some reason.) 10) You're done!
Note that this method has the innate drawback of not being able to recolour the hitcircles, so all of the circles will be monochrome and will have to be have the hitcircle recoloured before merging the layers. However, this is no longer an issue on the Cutting Edge build...
FOR BETA/CUTTING EDGE BUILD USERS:
1) Go into the folder of the skin you wish to perform this on. 2) Create a new, blank image. 3) Save as "sliderendcircle.png" 4) You're done!
This method allows you to keep your combo colours and is more or less the objectively superior way to do this. However, if you don't have supporter and want to play multiplayer or just have general issues with the Cutting Edge build as a whole, you may have to use the former method and wait for Peppy to release it in the near distant future.