Properly merging multiple .stl for 3d printing

[Anonymous]

Hi everyone, I'm pretty new to meshmixer and 3D modelling,

I'm trying to merge multiple parts of an action figure, to be able to 3D print it in a single session. The pieces are cut and have aligning pins to make assembling easier, so as an example there are holes in the torso to insert arms, legs and the head. The problem is that when I move the objects close to each other and then use the combine function, the holes are not filled and the pins tend to "sink" into each other.  Is the only solution making it solid? I've already tried that and it drastically reduces the quality of the .STLs, even while setting it to "Accurate" and increasing mesh density and Solid Accuracy to the maximum. I've already tried to export the finished and "unsolided" model to a slicer software, and when looking inside of it I can clearly see that there's some void space between the holes and aligning pins, and some aligning pins are inside the torso; I'm pretty sure that those would make the print fail. Am I doing something wrong, or even skipping something that needs to be done? What can I exactly do?

Thanks in advance

EDIT: Just to make it clearer:

[Anonymous]

Note: In MakeSolid you can set a higher SolidAccuracy and MeshDensity than the default sliders' max: Either by numerical input (for these parameters or their CellSizes) or dragging the sliders while dragging slightly up/downwards over the max. This might give a better result for the overall quality but does not fill the gaps (might be even worse).

So you need to construct an intersection of the parts to get a solution keeping the exterior mesh:

1. EDIT/GenerateFaceGroups and set the sliders to get a single group for each of the male contact surfaces (ignore the dowel) 
2. In SELECT select the male contact group by double click and add the dowel using the selection brush
3. On this selection run Deform/Transform and pull the blue Z arrow so the orange surface will intersect the female surface totally. Drag the white center cube to scale it down until the orange surface doesn't intersect the exterior of the female part (maybe you need to use the red and green arrow to change the position too).
4. Accept and leave Select. Activate male and female part (Press Shift to activate a second object).
5. Now do EDIT/BooleanUnion.