A sequence of single femtosecond pulses is used to create a pattern of laser affected spots at increasing depths below the surface of transparent biopolymer samples. Materials with different water contents and mechanical strengths, gelatine, chitosan, synthetic polyvinyl pyrrolidone, and biopolymer-polymer blends, are irradiated near the edge of the sample with an amplified Titanium:Sapphire laser (800 nm) delivering 30 fs pulses through a 0.45 numerical aperture objective with energies of 100-3000 nJ. The micrometric modified region is observed by optical microscopy perpendicularly to irradiation. Self-focusing and optical aberration are major factors controlling morphology and size of the created spots..