Sibelius has a very handy plug-in when you are dealing with real-time input and/or importing MIDI files.
Renotate Performance Plug-in
There is a plug-in called Renotate Performance. It does an amazing job of renotating and simplifying notation.
I also use it when step entering notation. It will often correct mistakes that I make such as placing quarter notes over beats 2 and 3 in 4/4 time. It is an amazing tool. It is a snap to use and if the change is not what you want just undo it and return to the original.
Applying the Renotate Performance Plug-in
I entered the following notation in real-time using Flexi-time.
Here’s what the Renotate Performance plug-in produced:
To run the Renotate Performance plug-in:
1. Select the source notation. You can select one or more bars and up to two staves at a time.
2. Choose Plug-ins > Simplify Notation > Renotate Performance
3. When the dialog box came up, I checked the Overwrite option. If you don’t check this box, the renotated version will be placed in a new staff.
I find that this plug-in is tremendous especially if you are playing in real-time and want to quickly clean up the notation.
Limitations
You can’t apply the plug-in to multiple staves. You are limited to 2 staves at a time. And, sometimes it will make adjustments to the notation and change the actual rhythms. When this happens, I undo the plug-in and make the edits manually.
Check out this handy plug-in.
Making the Most of Notation Software 