Fs-lasers are widely used for microsurgery and micromachining. Due to nonlinear interaction of ultrashort pulses with tissue or matter precisions of a few μm can be achieved. But particularly in the field of surgery this precision can not be obtained as the devices for diagnostics and treatment have to be changed due to separate systems. We show a combined system of a fs-laser and a Fourier-Domain optical coherence tomography (FD-OCT) enabling to cut and image the region of interest alternately. The FD-OCT offers non-invasive imaging at an axial resolution of 6, 2 μm and a transverse resolution of 3 μm in air which is comparable to the interaction zone of the fslaser-pulses. OCT-aided subsurface cutting is successfully demonstrated on biological ex-vito samples of porcine cornea and larynx. Furthermore it appeared that in situ OCT imaging enables to monitor cuts produced with pulse energies close to the energy threshold. In conclusion, this setup demonstrates the potential of a system combining cutting and OCT imaging within the same optical setup without the need of changing devices.