Multicellular structures are abundant in biology, from bacterial colonies to tissues. Characterizing and ultimately controlling these complex multicellular systems requires us to work across scales, from single cell interactions to flows and dynamics at the continuum level. In this talk, we will start at the resolution of single-cells, where in contrast to ordered crystals, it is less obvious how one can reliably distinguish two amorphous yet structurally different multicellular materials using single-cell positions alone. Working with only the local topological neighborhood information, we introduce a topological earth mover’s distance, allowing us to find interpretable reconstructions of equilibrium and nonequilibrium phase spaces, recover temporal ordering, and find embedded pathways from static system snapshots alone. Applications of this framework include finding organizing principles for epithelial cell layers and distinguishing species of bacteria from the architectural properties of their biofilms. Moving to larger scales, we will investigate the global morphology of bacterial biofilms growing in shear flow. We find that single cell interactions with the flow, together with nematic growth are sufficient to explain the peculiar shape which the growing biofilms take, and that we recover this behavior with a minimal continuum model. Finally, we will introduce a programable bacterial system, where synthetic cell-cell adhesin logic allows precise control of interfacial patterning on the macro-scale, together with a minimal continuum model which can predict experimental behavior.