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It actually is free unless you make more than 5k a year from it or something like that!
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I second Fusion360, which seems to be quite popular in the printing community
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Before going away from Blender, did you try doing a remesh in the sculpt mode using a very small voxel size on the combined object? Remeshes are really good at eliminating a lot of errors, but can take a while at small voxel sizes for large objects.
Another package to check out if you don't want to continually shell money to Autodesk is Alibre. It doesn't do STL import, but it is far easier to use than FreeCAD, and at only $150 (sale price) for the base modeler is a heck of a bargain for a perpetual license. The array options might make recreating your part relatively simple - I don't know. It has a free trial option, and is very close to SolidWorks in operation.
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I'm going to take you literally here:
CodeWraith wrote: object
And suggest purchasing ZBrush (in it's latest incarnation). Two reasons. Number one, perpetual license. Number two, I don't own it. But would like to know how good it is ... and get that information from a fully vetted CP Lounge denizen who gets bonked on the head frequently.
I'm doing a study you see ...
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I believe a full license is $895 now. Not super cheap!
Having used ZBrush and Blender, Blender's interface is so far superior to ZBrush I never want to go back. Yes, you can do anything in ZBrush. But you will spend orders of magnitude more time learning how to do so. And the mouse defaults (which can't be changed?) are ass-backwards to an Infuriating extent!
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I use OpenSCAD, it's a coding like language for creating 3d objects.
As a software developer by day, I find it rather easy, simply because I understand methods, loops, if's and objects.
To give you an idea of the language, something like this:
for(i = [0:9]) {
translate([i * 10,0,0]) cylinder(d = 5, h = 50, $fn=50);
}
would give you 10 identical 5mm wide by 50mm high cylinders, at 10mm distance apart on the x axis.
It can generate stl files for passing to the slicer. I have yet to have a problem with the slicer thinking the internals of any object is empty, and I have no problem in overlapping objects (I commonly place objects 0.1mm inside each other).
I also like that I can split complex parts into their own modules (methods) and then preview the entire printed object inside openscad, then print off each section by itself. I've found I've been able to do joins between components far better and more accurately than by simply slicing a model into two using the slicer.
To make things easier, there is also a community of people who design parts inside OpenSCAD. From simple libraries like a triangles library, to more complex libraries like gears, which can all be downloaded for free as well.
As for what I'm doing with the pieces I print, well I'm building a full sized functioning jumbo jet (boeing 747-400) simulator. I'm printing panels, controls, buttons and switches (the sort that you can't just get at your local electronics stores), and every piece has been designed with OpenSCAD.
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harvyk0 wrote: I'm building a full sized functioning jumbo jet (boeing 747-400) simulator
would love to see pics of the final product, or even an article. Sounds like fun.
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TinkerCad.
Free, simple. I use Fusion 360 occasionally but TinkerCad gets me 90% of the stuff I need to print.
It will import your STL files. I slice with Cura and rarely have an issue.
Fusion 360 has a free tier but finding on the site seems to be purposefully difficult.
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Using using STL files for anything other than export can cause problems. I use DesignCad Mechanical (free from RS Components) and always save my work in the default format, exporting to STL only before slicing. I've never found a reliable way of importing an STL file and modifying it.
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Do your design in Blender and then load the model into MeshMixer (another free software package from Autodesk). Select to "Convert to Solid". This will re-mesh the object and remove all internal faces. The mesh will be converted to triangles (no other polygons are allowed), but that isn't a problem for most slicers.
Of course, MeshMixer can do much more than that, but it sounds like this is what you need.
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I suggest OnShape, a fantastic completely web based cad.
There is the free version which, as the only limitation, makes all your documents public.
It is really well done, it is parametric and it has a lot of professional features.
It also allows you to import STL files (I've never done that), but I don't think it has any specific cleaning functions.
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( My joy of 3D printing was dear windows doing one of it's "you haven't touched the mouse in _hours_ I'll just force a re-boot now" half way thru a print. )
3-D cad, - now, I started as a machinist. We cut stock apart, cut shapes, weld or bolt together. I like Solidworks, it does that well, you may want something that acts more like molding clay.
So, you need to consider the shapes you are making and how you are defining them. For my work, I've been using Alibre. It's not what I'd take for full time, but closer to $1K than $5K.
If you have a _fast_ connection, OnShape can do a good job. If you don't care about assemblies, ( in the above, I could model a bicycle as component parts then assemble it. And turn the crank - probably have that turn the rear wheel, I don't think I could get a derailleur to shift the chain. )
But for just parts, and you _could_ model the bicycle as one part, there are several free programs, ( FreeCAD looks good, but given I can't do assemblies, I've not really worked at it. )
Several of the big cad systems ( Catia and Ansys, I think Autodesk not sure who else ) have free 3d part modelers some may have the more "plastic" approach I expect lots of people to want. Their free offerings are limited, but some only in that they don't handle assemblies, and they are stable. Good code base under them.
If your needs are more than that check our Rhino.
Have fun.
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try rhino3d
good importer and exporter
jm
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Metal: ductile and conductive but uncommon. Poisonous. (6)
"I have no idea what I did, but I'm taking full credit for it." - ThisOldTony
"Common sense is so rare these days, it should be classified as a super power" - Random T-shirt
AntiTwitter: @DalekDave is now a follower!
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"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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I take it that means you have got it? 
"I have no idea what I did, but I'm taking full credit for it." - ThisOldTony
"Common sense is so rare these days, it should be classified as a super power" - Random T-shirt
AntiTwitter: @DalekDave is now a follower!
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Yes but I've done two this week
"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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Well, it's only Wednesday - there's still room for you to do another two? 
"I have no idea what I did, but I'm taking full credit for it." - ThisOldTony
"Common sense is so rare these days, it should be classified as a super power" - Random T-shirt
AntiTwitter: @DalekDave is now a follower!
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There's really only a handful of us that do the CCC now.
"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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Or a handful that get it right and are prepared to set? Who knows how many around the world are scratching their heads right now...
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I think it's the "prepared to set" bit that scares 'em off.
Wish there was a way to avoid that without having a single dedicated setter, and the whole idea of the WSO bit was not to duplicate the Dalek's posts when he ran away to hide ... 
"I have no idea what I did, but I'm taking full credit for it." - ThisOldTony
"Common sense is so rare these days, it should be classified as a super power" - Random T-shirt
AntiTwitter: @DalekDave is now a follower!
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What happened to DD on here ? did he just leave ?
"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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