A while ago, a friend of mine gave me an STL file from a scanner. It was a 3D bust that he wanted to print. Unfortunately, being a scan, it had some errors in it that replicator G could not deal with. However, I didn't discover the error until I told him printing out his file would be no problem. That was before I discovered the print had several errors which made a very pretty bust look like some sort of mythical spiked creature! Since the file was a scan rather than a drawing, it was impossible for me to manually repair. It is in this way that I was introduced to the concept of a "manifold" print.
Enter the NetFab program. One of it's features is the "repair" feature. Just import your .STL file. Then select the "repair" process. If there are relatively minor problems such as small gaps this program can usually find them and use an average value which is usually good enough for a print. The basic version is free to use, works well and works quick. As you may have guessed from my list of printing steps, I'll take any time savings I can get!