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I try to connect these two but Ctrl + J doesn't work and because its all in one mesh Boolean doesn't work either, the two meshes are in one layer.

enter image description here

As you can see, they re not connected

enter image description here

I would like to delete this part here:

enter image description here

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    $\begingroup$ Hi and welcome to Blender Stack Exchange. First, you wrote that you want to join two meshes, but they are actually one mesh? That doesn't make much sense, could you please... uhm... elaborate on this a little more? A screenshot in edit mode would be also quite helpful. Please use the edit link below your question to add more useful information. $\endgroup$ – metaphor_set Oct 27 '18 at 15:31
  • $\begingroup$ maybe there are 2 meshes in the same object, but yes, it lacks precision, to say the least... $\endgroup$ – moonboots Oct 27 '18 at 15:49
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    $\begingroup$ changed "join" to "connect" guess that's right word here to use ... and added some more pictures $\endgroup$ – Raoul L'artiste Oct 27 '18 at 15:55
  • $\begingroup$ As Robin Betts said, Bridge Edge Loops is faster than join the vertices manually, please check my answer again ;) $\endgroup$ – moonboots Oct 27 '18 at 17:46
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If you don't want to keep ngons, which are evil, here is a basic way to do it:

  • Select the face and press X > Only Faces.
  • Now the face is gone.
  • Join the vertices of the base of the cylinder with the vertices of the faces with W > Bridge Edge Loops.

enter image description here

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  • $\begingroup$ I'd just like to point out that ngons have a place...albeit only when nothing is bending. (: $\endgroup$ – SilverWolf - Reinstate Monica Oct 27 '18 at 20:49
  • $\begingroup$ perhaps, I just tried to give the simplest and most general answer, most of the cases we should avoid ngons, and even tris if possible $\endgroup$ – moonboots Oct 27 '18 at 20:55
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you can use the knife tool. If you want to eliminate the extra faces.

press k for the knife tool and click around the cylinder shape.

once the hole you like has been created.

use alt-m to merger vertices.

select one of each vertices you want to merge. press alt m.

and choose at first, or at last, to maintain shape, depending on what order you select your two vertices.

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