Direct-write soft x-ray lithography with an similar to 50 nm diameter beam is used to pattern features in hydrogen silsesquioxane (HSQ) thin films. Scanning transmission x-ray microscopy of the undeveloped patterns (latent patterns) at the oxygen K-edge reveals a two-stage cross-linking mechanism. Oxygen and silicon near edge x-ray absorption fine structure spectra of latent patterns show an increase in oxygen content and no change in silicon content within exposed regions. A dose and thickness dependent spatial spread of the cross-linking reaction beyond the exposure boundaries is observed and quantified in detail. Strong area-dependent exposure sensitivity (attributed to cross-linking beyond the exposed region) is observed in latent patterns. A lateral spread in the cross-linking of >70 nm (full width at half maximum) is observed on both sides of the lines created with 580 eV x-rays (lambda=2.14 nm) in 330 +/- 50 nm thick HSQ films at low dose (0.6 +/- 0.3 MGy, 27 +/- 12 mJ/cm(2)) (1 MGy=10(6) J/kg absorbed energy). At a higher dose (111 +/- 29 MGy, 5143 +/- 1027 mJ/cm(2)), this spread increased to 150 nm. Preliminary results indicate that latent line widths increased with increasing delay between film spin-coating and exposure. Sharper lines are observed after room temperature development of the latent HSQ patterns in NaOH/NaCl solution (onset dose of 3.9 +/- 1.0 MGy, 181 +/- 36 mJ/cm(2)) due to the removal of material below a critical degree of cross-linking. Given the short range of low energy secondary electrons in condensed media (<10 nm at <= 580 eV), the observed spread is likely due to the propagation of reactive ions or radicals beyond the exposed regions. (C) 2010 American Vacuum Society. [DOI: 10.1116/1.3514124]