Cutting a 1D Line:
We can cut a 1D line via 0D point.
if we want to cut a 1D line via a 1D line.
we have to move 1 dimension up that is in 2D
(Image for 1D Line cut by 0D pt.)
(Image for 1D Line cut by 1D line)
Cutting a 2d Plane:
We can cut a 2D plane via 1D Line.
if we want to cut a 2D plane by a 2D plane
we have to move 1 dimension up that is in 2D
(Image for 2D plane cut by 1D line)
(Image for 2D plane cut by 2D plane)
Cutting of a 3D Cube:
We can cut a 3D Cube by a 2D Plane
So the question arises that
Can we cut a 3D cube by a 3D cube?
And if yes then how ?
For it we may require 1 more dimension (4th dimension).
(Image for 3D Cube cut by 2D Plane)
So how can we do that!
In all the cases sizes doesn't matter:
Size of a Line doesn't matter that if we cut a Line by another Line. And Size of a Plane doesn't matter that if we cut a Plane by another Plane.
Is it same for Cubes? Does Cubes size also doesn't matter. Can we cut a Cube by another Cube(Like a Plane cuts a Cube) and that another Cube's size can by 10x, 100x, 1000x etc ?
I think understanding how a 3D Cube is cut by a 3D cube help me to understand (or say visualize) what 4th Dimension is?
The short answer to your question, in your terms, is that the 3D cube cut by a 3D cube will be a be a 2D thing in the fourth dimension.
Your deeper question
is a hard one. Mathematicians study the geometry of $n$ dimensions by using algebra. When $n$ is $1$, $2$ and $3$ you have the number line, the plane with points $(x,y)$ and 3D space with points $(x,y,z)$. There you can match algebraic arguments with pictures. For four dimensions, work with points $(x,y,z,w)$ - but there and in higher dimensions all you have is the algebra.
The algebraic answer to your "cutting" question is that in general, if you have subspaces (what you call "cubes") of dimensions $k$ and $l$ living in $n$ dimensional space they will cut each other in a subspace of dimension $k+l-n$. That pretty much covers all your examples.
But visualizing this is not something humans are naturally equipped to do. My thesis advisor, Andy Gleason, once told me he would give a lot for one good look at the fourth dimension.