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I want to use the top half of the circle to make a cut but whenever I apply the boolean modifier, the circle just stays there and becomes attached to my other object.
I've managed to make the cut in a standard cube but not sure why it's not working for this...?
That's because of the limitation of approach of how inner/outer surface are calculated in Boolean modifier. Current Boolean uses Carve library. Carve will perform boolean operation only if the intersection of two meshes is a closed loop of edges.
As shown in your image, the object is not a closed manifold one, which confuses the edge classifier. This is listed in Boolean modifier limitation.
To solve this, I suggest adding a Solidify modifier on top of Boolean modifier, with a very small Thickness Value (such as 0.00001). After applying both modifiers, you can press W > Remove Doubles to clean the mesh, and select all faces, then press Ctrl N to correct normals. (This sounds like a trick, but it works in this case, since there's nothing you can do with the current Boolean approach, which got its own advantages as well as limitations)
By the way, in the coming 2.70, Boolean modifier supports ngons, which means you can generate much better and cleaner results (as shown in above image). You may want to give it a try.
There might be a problem with the normals. Select the Cylinder and go into edit mode, and recalculate the normals, Ctrl N. Do the same for the box object.
Select the Box like object (not the cylinder).
Add a boolean modifier
Select the cylinder as the Object in the Boolean Modifier settings
You need to set the boolean modifier to difference.
If you have other modifier on the mesh you might need to apply those first, before you apply the boolean modifier.
Try the triangulate modifier on both shapes.
I also had the problems with larger models that are may of not perfect quality. I also made some afford in building the model with quads or remiss all didn't work.
In these cases put a triangulate modifier on both shapes and place the boolean modifier afterwards.
I think I've gotten around that by selecting just the faces which are going to be cut and subdividing them a few times prior.
I'm suspecting that the additional geometry helps give the Boolean operator more to work with.
I did get a slight anomaly on the inside of the wheel well but looks easy to fix if I feel like it and it'll be hidden by the tire anyhow.
Overall I'm finding that additional geometry helps with a lot of things in Blender and I'm slowly getting better at targeting where and how I place that.
I had a mesh that instead of doing a union It just combined the two meshed like in a join.
I used the overlap threshold to change how much the mesh is cut into.The overlap threshold is in the Boolean modifier.
I faced exactly the same issue. I generated the cylinder by extrusion of a circle. My problem was that the circle was originally placed exactly on the face of the other object. To solve this, I just moved the cylinder a bit in the normal direction to prevent the edges of the original circle to be at the intersection.
