Investigations on some aspects of thermal etching of silicon and polymer substrates are presented. Microscopic mechanisms of thermal degradation of substrate materials commonly applied in microelectronics and microsystem technology by means of radical containing downstream plasma are examined. The role of molecular constituents of the downstream gas flow for the etching process is considered in detail. Transport of free radicals through very high aspect ratio structures is demonstrated experimentally and interpreted in theory. Investigations presented here were performed by means of the Nanojet setup (reported in this volume).