Longitudinal inhomogeneity of tracks inscribed in a YAG crystal and the statistics of nonlinear transmittance of the writing beam is studied under conditions of direct femtosecond laser writing in non-thermal mode. Nonlinear transmittance fluctuations inherent in the laser writing were discovered, and their correlation with track inhomogeneity is established. A model of femtosecond laser writing in crystals is built that includes three modes of plastic deformation in the laser impact zone. The modification threshold of the femtosecond direct laser writing is identified with reaching yield stress.