Element can import AE masks, which you can extrude, bevel and texture.
It's very unclear from your question what is wrong with your workflow (there is no "pencil tool" in After Effects) but I'll take a guess.
It sounds like you are creating a logo in Illustrator or Photoshop, importing that to AE and expecting Element to read it. It won't.
Element can only read After Effects masks, After Effects text layers, or external 3D formats like .obj. If you import a 2D graphic to AE, you will need to convert its outlines to masks by auto-tracing it. Alternately, you can copy and paste paths from Illustrator to AE.
What kind of file are you trying to use? What version of AE? What OS? What is your workflow? Did you watch any Element tutorials? Without knowing something more than 'it's broken' we have a hard time helping, except that I believe Element uses masks....
You are not understanding the workflow, I'm afraid. Element 3D does not use splines from C4D, but it can use real mesh geometry. So yes, you will need to create an Extrude object in C4D if you go that route and also make sure to enable the Save Polygons for Melange option in the C4D preferences. Otherwise Element can use masks as contours, but how well that works will depend on your masks and the settings you use. Nobody can help you without seeing those settings and masks, though, so hurry up providing some of that info as screenshots.
Just a normal png.
I'm running on After Effects CC.
My graphics card is 3D compatible.
Yes, I've watched a lot of tutorials but non that covers what I need.
I select my logo, layer, auto-trace.
That masks my logo, then I go into the Element scene set-up, add all the things I need but when I export it back t o AE it's messed up.
The sides are shorter than they should be like it's cropped.
You are looking for simple one-button solution that doesn't exist. Your contours need to be properly cleaned up and sorted suitably to create the contours in the correct order. A simple overlapping point can completely whack out things. Auto-Trace is merely an auxiliary tool to create masks, but nowhere is it written that they are perfect and usable to create clean extrusions.
No it wasn't that.
I found the solution.
I had to in to properties all sort if options.