If I am right in assuming the undupe CAL only removes exact duplicate notes, how does one remove say a short note that may be hidden behind a longer note but not necessarily the same length or start time?
Pete.

If there is only a few of them you'll probably hear them as being louder, so just slide the overlapping note up or down , delete the offending note and put the original back in place. 
 
Not sure if this works too, but try highlighting all the notes using the left hand keyboard GUI and then move that row up or down temporarily to see if the underneath notes stay behind?? 

I'm afraid option one would not be a consideration as that is how I found hidden notes initially. That works for one or two notes but not for hundreds of notes. We need something like a CAL that deletes hidden notes.

If you use the EDIT:Select: By Filter then select only the Note option (quickest way is to use the NONE box at the bottom right first, then just tick the Note box) you can specify what notes by length and/or velocity...then simply press delete.

Did this happen because of quantizing a track? Hopefully his trick works otherwise it might be way easier to re record the part and try a different quantizing setting. 

Undupe has a tolerance value for the start times; should still work.

Another option to using Cal - which might not even work in this case, is to use the staff view.
 
Any duplicate notes in time (length is irrelevant) will appear as a double note on the stalk.
 
Click each duplicate and delete it. This will in all probability delete both notes, but don't panic - simply hit ctrl + z and just ONE of the delete notes will be restored.
 
This might be of the correct length or it might not, so go into the prv, check and if necessary slip edit to the correct length and move on to the next double.
 
Have the Staff View & Prv arranged horziontally and zoomed to the same resolution to aid navigation.

I don't know why folks need to mess with Undupe and the trial and error way it operates...As I wrote earlier just use the superb tool already in Sonar... Select by filter..it is far more "surgical" and for a lot more than note removal.

joden
I don't know why folks need to mess with Undupe and the trial and error way it operates...As I wrote earlier just use the superb tool already in Sonar... Select by filter..it is far more "surgical" and for a lot more than note removal.

 
Maybe because, say, a 3 beat-long note (with a very low velocity) might be hidden behind a 4 beat-long note? I don't know.

You can also select via velocity as well...I have used Undupe and it sorta kinda works, in a "down and dirty" way ..but I have found the Select by filter to be , more accurate and in the end, quicker. Many times in Undup I removed notes I needed.
 
As an example, I just start with low velocity and work up, I mean if it is hidden,  and has the same start time, chances are it is not even being heard anyway..so I would look at a PRV determine what is the shortest note I want to keep and go from there...
 
EDIT: TBH, I am not saying Undupe is useless, nor criticising folks for using it, just there are other tools available