I’m a big fan of Simplify 3D. Its a commercial software but its worth every 149$ that it costs. If you digging deeper into 3D-Printing you can take your pre-processing to the next level. I had the issue, that when printing a model with solid infill (100%) and 0.1mm layer height on an Makerbot Replicator 2 the base would show gaps in between the extrusion lines.
As the model should be water tight I made a simply test – blowing through the model. It was not watertight, you could blow “through” the wall. Holding it against the light you could also see that there were gaps in between the extrusion lines.
One thing with Simplify 3D is that you have a lot of parameters, which also interact from time to time and sometimes its unclear what change bring the solution.
I fiddled with a lot of parameters, including extrusion width, gap fill or infill extrusion width. What helped was to tweak the parameter “Extrusion multiplier” to 1.10 (formally 0.8). Like this I can make really solid model with out gaps of holes between the extrusion lines.