In molecular communication, a group of biological nanomachines communicates through exchanging molecules and collectively performs application dependent tasks. An open research issue in molecular communication is to establish interfaces to interconnect the molecular communication environment (e.g., inside the human body) and its external environment (e.g., outside the human body). Such interfaces allow conventional devices in the external environment to control the location and timing of molecular communication processes in the molecular communication environment and expand the capability of molecular communication. In this paper, we first describe an architecture of externally controllable molecular communication and introduce two types of interfaces for biological nanomachines; bio-nanomachine to bio-nanomachine interfaces (BNIs) for bio-nanomachines to interact with other biological nanomachines in the molecular communication environment, and inmessaging and outmessaging interfaces (IMIs and OMIs) for bio-nanomachines to interact with devices in the external environment. We then describe a proof-of- concept design and wet laboratory implementation of the IMI and OMI, using biological cells. We further demonstrate, through mathematical modeling and numerical experiments, how an architecture of externally controllable molecular communication with BNIs and IMIs/OMIs may apply to pattern formation, a promising nanomedical application of molecular communication.