Detection represents an important limitation of accurately estimating population size, abundance, and habitat suitability for wildlife, which can be especially true for cryptic animals. Moreover, for reptiles, juveniles are often less likely to be detected than later life stages. In the case of invasive species, preventing false negatives early in the invasion process can be critical for improving outcomes of control measures. We evaluated habitat structure in relation to catch per unit effort (CPUE) and mean size of trapped invasive brown treesnakes (Boiga irregularis) on Guam. We used a 5‐ha enclosure containing a known, closed population of brown treesnakes to identify key habitat variables that related to CPUE and mean size of trapped snakes over six years. We then tested the relationship of those variables to CPUE and mean size of trapped snakes at three sites with suppressed snake populations as a proxy for low‐density populations anticipated to occur during early detection of invasive populations. We found that a coarse measure of habitat structure represented by three forest types correlated with trap detections, as well as finer measures of habitat structure, such as distance to nearest branch and the type of trap support structure used. On average, smaller snakes were captured in traps placed higher in the tree canopy. Some, but not all, habitat variables identified as predictive of CPUE and mean size within the enclosed population pre‐suppression were also predictive at the snake‐suppressed (low‐density proxy) sites. Habitat structure around the sampling unit (a trap) affected detection probability and the size of detected individuals independently of the demographic structure of the population. Measuring wildlife‐habitat relationships of invaders in their novel environments may be one method to improve early detection during invasive species management.