in UG there is an export option named "heal". as an output you are getting geometry in UG format with some features (like very small areas, etc.) removed. it helps a little bit but does not remove the problem completely so you will have to do some work on your own. I do not know if such an option exists in CATIA, due the limited number of licenses we are using step as a format to move geometry from CAD to FEM. I know ANSYS ICEM/CFD is now integrated with ProE but as I am not using ProE I can not say anything more.
ANSYS invested recently in meshers a lot and I have to admit they made a step forward. their Workbench works with the various geometry formats much better than it was the case in the past.
I can also recommend Hypermesh as pre-processor. its capabilities are really impressive.
the problem is those tools, as most of the CAE software, are quite expensive.
you can also create your own mesher(s). it takes time, it will not be as fast and efficient as the professional tools (I checked this on my own somewhere in the past
) but it will give you much better understanding of the tool, the math behind it, its strong and weak points and thus will make you a much better engineer.
regards