A programmable controller for a 2D Lissajous scanning fibre microscope is described. Source motion is based on a vibrating cantilever formed by dip-coating two cylindrical silica fibres. Orthogonal modes are excited by a piezoelectric actuator oriented at 45° to the principal axes. Back-scattered signals are detected using a mode-stripping photodiode to collect cladding modes in a dual numerical aperture confocal scheme. Optical feedback is generated by a shaped reflecting aperture with amplitude-coded reflectivity. Electrical pulses from the detector are separated into low- and high-mode feedback signals using window detectors. The low mode is excited at resonance using a phase-locked loop (PLL) containing a voltage-controlled oscillator (VCO). The high mode is driven off-resonance at a frequency derived from computer control of a second VCO. Amplitudes are corrected, and common frequency signals derived from the two motions using divide-by-N circuits are synchronised using additional PLLs. Programmable generation of Lissajous figures and imaging with dynamically variable scan density are demonstrated.