We fabricated several microstructures, such as buried gratings, surface gratings, surface microcraters, and microchannels, in bulk poly(methylmethacrylate) (PMMA) and poly(dimethylsiloxane) (PDMS) using the femtosecond (fs) direct writing technique. A methodical study of the diffraction efficiency (DE) of the achieved gratings was performed as a function of scanning speed, energy, and focal spot size in both PMMA and PDMS. An optimized set of writing parameters has been identified for achieving efficient gratings in both cases. The highest DE recorded in a PDMS grating was ~10% and ~34% in a PMMA grating obtained with an 0.65 NA (40X) objective with a single scan. Spectroscopic techniques, including Raman, UV-visible, electron spin resonance (ESR), and physical techniques, such as laser confocal and scanning electron microscopy (SEM), were employed to examine the fs laser-modified regions in an attempt to understand the mechanism responsible for physical changes at the focal volume. Raman spectra collected from the modified regions of PMMA indicated bond softening or stress-related mechanisms responsible for structural changes. We have also observed emission from the fs-modified regions of PMMA and PDMS. An ESR spectrum, recorded a few days after irradiation, from the fs laser-modified regions in PMMA did not reveal any signature of free radicals. However, fs-modified PDMS regions exhibited a single peak in the ESR signal. The probable rationale for the behavior of the ESR spectra in PMMA and PDMS are discussed in the light of free radical formation after fs irradiation. Microchannels within the bulk and surface of PMMA were achieved as well. Microcraters on the surfaces of PMMA and PDMS were also accomplished, and the variation of structure properties with diverse writing conditions has been studied. [c] 2010 Optical Society of America OCIS codes: 050.1950, 130.3120, 220.4000, 300.6450.