A multi-chip module (MCM) that includes alignment features is described. This MCM includes at least two substrates having facing surfaces with positive features disposed on them. Note that a given positive feature on either of the surfaces protrudes above the surface. Furthermore, the two substrates are mechanically coupled by these positive features. In particular, a given one of the positive features on one of the surfaces mates with a given subset of the positive features on the other of the surfaces. Additionally, the given subset of the positive features includes two or more of the positive features.