What can I do to get neater prints? (Photos included)

[Sloyfa]

This file is something I had someone design for me, and then I put it right into my Makerbot Print app. I've used Makerbot Print for everything I've printed in the last 3 years, with great results, and so I was surprised that I couldn't eliminate these issues by adjusting the print quality, layer size, heat (both increasing and decreasing), and speed. I even went to an old computer and used the old version of Makerbot Desktop with all the settings that I'm used to there, too, including the "high quality" print setting.

I have 12 of these wheels printed now, all using different settings and printers, and while they each vary a little they all have the problems you see in the photo. That's why I'm wondering if there is something about the file it'self that I should change.

Is there a way I can "clean up" or "neaten up" the print file myself with a software? So I can do this in the future, when I need to?

I have Netfabb free, and Simplify3D. I'm a novice at both, but glad to learn things that I'll use in the future.