Corn stover was pretreated with aqueous ammonia in a flow-through column reactor, a process termed as Ammonia Recycle Percolation (ARP). The aqueous ammonia causes swelling and efficient delignification of biomass at high temperatures. The ARP process solubilizes about half of xylan, but retains more than 92% of the cellulose content. Enzymatic digestibility of ARP-treated corn stover is 93% with 10 FPU/g-glucan enzyme loading. The SEM pictures and FTIR spectra confirm swelling and delignification effects of the ARP process. The X-ray crystallography data indicate that the basic crystalline structure of the cellulosic component of corn stover is not altered by the ARP treatment. Low-liquid ARP can reduce the liquid throughput and residence time to 3.3 mL/g-biomass and 10-12 min, without adversely affecting the overall effectiveness. The low-water ARP achieved 73.4% delignification and 88.5% digestibility with 15 FPU/g-glucan. The ethanol yield from the SSF of low-liquid ARP-treated corn stover using Saccharomyces cerevisiae reached 84% of the theoretical maximum. Successive operation of a hot-water treatment and the ARP was applied as a method of biomass fractionation. The two-stage process separated xylan in the first stage (84%) and lignin in the second stage (75%), resulting treated solid that contains 79% glucan.