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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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He got a "safe seat" as a Tory in the luton council elections - and felt that some of his comments here wouldn't necessarily be seen in a good light by his voters. So he stopped posting for a while, then posted a very anti-Gypsy comment on twatter or farcebook and managed to turn a safe seat into a lost seat during the biggest swing to his party in 50 years ...
He hasn't been back since ...
"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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DerekT-P wrote: how many around the world are scratching their heads
At least one in Woking. 
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And one further north 
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Nottingham and its environs is an area I am not familiar with.
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Oh, they are strange up there - it's all mushy pea and Whippet sandwiches*. 
* Well, not really. But heck, I get the mickey taken about sheep so fair's fair ...
"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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My son lived up there for a while, and when he came back home he was forever enthusing about "chips with gravy".
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Gods little acre is one of its nicknames
"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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Well, COPPER fits but doesn't seem very cryptic?
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You are very close for the first part
"I didn't mention the bats - he'd see them soon enough" - Hunter S Thompson - RIP
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That's probably because it's wrong ...
"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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DerekT-P gave me the clue:
Metal: CU (copper)
Uncommon: RARE
CURARE a deadly poison.
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