Although femtosecond laser cell surgery is widely used for fundamental research in cell biology, the mechanisms in the so-called low-density plasma regime are largely unknown. To date, it is still unclear on which time scales free electron and free radical-induced chemical effects take place leading to intracellular ablation. In this paper, we present our experimental study on the influence of laser parameters and staining on the ablation threshold. We found that the ablation effect resulted from the accumulation of single-shot multiphoton-induced photochemical effects finished within a few nanoseconds. In addition, fluorescence staining of subcellular structures significantly decreased the ablation threshold. Based on our findings, we propose that dye molecules are the major source for providing seed electrons for the ionization cascade.