To assess a timber harvesting operations system incorporating the extraction of logging residues for supplying a biomass power plant, we developed a method to estimate the harvesting volumes and costs of logging residues from subcompartments with plus balances, including both timber and logging residue harvesting. We estimated harvesting volumes and costs using GIS (Geographic Information System) at Sano City, Tochigi Prefecture. Forest-registration data (stand ages, tree species, and site indices) and GIS data (information on roads and subcompartment layers) obtained from the Tochigi Prefectural Government were used in the study, as were 50-m grid digital elevation models (DEM) from the Geographical Survey Institute. These data were converted into 50-m grid raster data for consistency with DEM data. As a result, the minimum and average costs of a cut-to-length system with forwarders from subcompartments with plus balances were found to be 6,270 yen/t and 7,934 yen/t, respectively. Of the subcompartments, 16% were extracted as economically feasible subcompartments. In order to reduce costs, subsidy, stem extraction, and a whole tree logging system were considered. As a result, the average costs with subsidy were reduced to 6,566 yen/t, and 40% of the subcompartments were extracted. The average cost of stem extraction without branches was also reduced to 7,132 yen/t. The minimum and average costs of the whole tree logging system were significantly reduced to 1,794 yen/t and 3,658 yen/t, respectively. Moreover, costs considering timber extraction were also reduced. Therefore, the whole tree logging system may be more advantageous than the cut-to-length system for extracting logging residues.