Someone explain why this is

I’m trying to get my head around modelling in blender to 3D print. I don’t understand how once you have an Open box how to make it manifold? I want to cut a bunch of holes in this box for Windows when I check if I can print this object every single Edge is non manifold so exactly how do I make objects that have openings that I can 3D print. Another strange error is not flat faces a cut a hole in a a box face and suddenly that face is not flat how is that possible all I did was cut the surface using the knife feature.

Care to post a screenshot of your current mesh and the result you want to achieve? It’s a bit hard for me to understand your issue…

In general: Your mesh needs to be solid. So, if you’re working with an open cube, make sure the walls actually have thickness, e. g. by using a Solidify modifier.

Polygonal modeling is approximation and it’s a surface type modeling paradigm, we’re supposed to approximate curves and surfaces. When you define a continuous and connected surface with all its face directions consistent and pointing out, that encloses a solid - It’s manifold.

If you want to describe a hollow object, put another surface offset to the first one and have its faces pointing to the opposite direction of the first one. Those two then describe a solid between them and it’s still manifold.

If you have a hollow real life object and you drill a hole through the solid material to get to the inside, that object would then have one continuous and connected surface that you would have to model. The newly created hole connects the two with its surface. If that object is a house and it has a hole for the door, you can walk outside and run your finger on the wall, walk in, and still don’t need to lift your finger off to do so - it has one continuous surface.

Same with a coffee cup. It’s the form of the surface that holds the liquid, not because it has two surfaces.