Removing internal geometry before 3D printing I am pretty new to Blender but I looked at some tutorials on how to build my own structure etc. I found one Youtube video at about 2:05 minutes, where they select all inner vertices with some clicks and removes them afterwards.

Can somebody help me to redo this on my objects? I have for example two cubes and they intersect each other. My next steps are joining these two cubes, I click in edit mode on Mesh > Faces > Intersect 
Then I choose Self intersect and now I am losing track of the video, where he does Link select and inverts the selection and then magically he just removes the selected parts...

Can somebody help me on this a little.

If I let the internal geometry stay, my printouts in the printer get holes and other ugly stuff...

EDIT

Since I got now an answer where some people up voted but it is still not working in my example.

I added a screenshot 
Here I have two cubes moved against each other. The answer from Gwenn suggests to use Select > Internal Faces but in my case there is only Select > Interior Faces. I guess this is a typo but it is also selecting nothing. When I click on Select > Non Manyfolds there is also no selection :-(

After following some links and checking the '3D Printing Tools' add on, I found the check function there which tells me how many problems where found in before printing (visible in the screenshot). It says no Manyfolds, maybe thats the reason. But I still have the problem of empty spaces within the 3D print where the two cubes overlap.

Again, I just created two cubes and moved them against each other until they intersect.

The only possible solution by now is to use a boolean modification, Difference and select the second cube. In this case the overlapping part gets removed from one of the cubes. Not very handy but by now the only solution which works.
All internal faces can be selected by using Select > Internal Faces in the bar on the bottom of the 3D View in Edit Mode.

Since internal faces are Non-manifold geometry, you can also use the shortcut CtrlShiftAltM to select them, along with all other non-manifold geometry.

Once you have the offending faces selected, you can use Del>Faces to remove them without affecting the rest of your geometry.