To solve the blockage caused by silica during the hydrothermal conversion of rice hulls into acetic acid in a continuous flow reactor, the removal of silica from rice hulls and the retainment of organics by alkaline extraction were carried out in a range of pH values from 5 to 12 and temperatures from 30 to 85 degrees C. It was found that the efficiency of silica removal and organics retainment strongly depended on the pH value but was less influenced by the reaction temperature. Based on the individual behaviour of holocellulose, lignin, silica and extracts during the alkaline extraction, a two-step low-temperature pre-treatment for removing silica but retaining organics was proposed. Water washing was firstly performed to recovery a portion of lignin and extracts, and then alkaline extraction was operated to remove silica in the rice hulls. 92.1% silica was removed and 73.4% organics retained after the two-step low-temperature pre-treatment. The retained organics was treated by a two-step hydrothermal treatment and an acetic acid yield of 20.8%, similar to that from non-extracted rice hulls, was achieved. The obtained silica could be expected to be used as fine raw materials for the production of silicon-based products. (C) 2008 The Institution of Chemical Engineers. Published by Elsevier B.V All rights reserved.