Orangutan as an umbrella species is closely interlinked with sustainable forest management meaning that the protection of this species has implications on the protection of other species and maintain ecosystem stability. The total natural habitat required to support orangutan’s population could only be determined by the appropriate population size. It is associated with the carrying capacity to accommodate or fulfill the habitat requirements of a wildlife population. Selection and delineation of core and wilderness zones as habitat preference should be based on the results of preference test shown by the spatial distribution of orangutan population. Value of the coefficient of variation (CV) was used to observe the precision of the population estimation and to identify important ecological factors in selection of nesting trees. The study resulted in varied CV spatial values for various habitat types: 22.60%, 11.20%, and 13.30% for heath, lowland dipterocarp, and peat swamp forest, respectively. In the other side, CV temporal values for various habitat types were 5.35%, 22.60%, and 17.60% for heath, lowland dipterocarp, and peat swamp forest, respectively. This indicated that the population density in each type of forest ecosystems had a variation based on location and did not varied according to time of survey. The use of nest survey technique showed good reliable results in estimating orangutan population density. Efforts to improve the precision of estimation can be done by formulating r value as the harmonic average of nest production rates and t as the average of nest decay time per nest category. Selection of habitat preference and nest trees were influenced by food availability thus should form important consideration in conducting nest survey to avoid bias in estimating orangutan populations.