Help cutting and connecting parts

When working with mechanical CAD it's best to work with a CAD file format that can be reasonably edited. That is either the original source CAD files or at the very least, STEP files. STL files are for transferring information for 3D printing. STLs are not a suitable file format for sharing mechanical CAD information that needs to be edited.

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If you are attempting to edit the STL files I would guess that is your primary problem. That is the file format you were sharing before so assume you are doing it again. Do not attempt to edit STL files except as a last option.
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Please share the specific STEP CAD files for the parts you are working on.
Tdrone Open Source Coaxial Drone

A sketch of what you are attempting to do or the CAD work you have done so far would be a tremendous help.

And for others that may be interested, refer to the original posts here:
https://grabcad.com/questions/i-can-t-download-parts-of-a-model

https://grabcad.com/questions/i-need-to-download-individual-parts-of-a-single-assembly--1

https://grabcad.com/questions/help-designing--2

I commented once before:
"Just open the STEP file and then save it. That will create all the individual IPT files. That’s all you have to do..."

You have Inventor professional. Open the STEP file and then just hit "save". It will create all the IPT and IAM files for you automatically. These are the files you should be working with.

I must reiterate, The STL files are next to useless for what you are wanting to do.

These are the files you should be sharing and using: