It's incredibly complicated and every type of tissue has it's own specific mechanisms for forming it's 3D structure but the short answer is that there is an "ex

It's incredibly complicated and every type of tissue has it's own specific mechanisms for forming it's 3D structure but the short answer is that there is an "extracellular matrix" that forms a network of macromolecules using collagen, elastin, fibronectin, and a bunch more signaling and structural proteins that organize cell growth. The ECM starts developing in the fetus and figuring out how it grows from a few cells into a bunch of differentiated organs, muscles, bone, etc. is a core problem in embryology (biology in general, really). If we knew enough to make proper meat, we'd probably be steps away from a Jurassic park scenario.