Anthropogenic habitat loss and fragmentation are major threats to ecosystems and a focus in conservation. However, conservation is often limited to considerations of site-level processes neglecting the effect of the surrounding landscape that might limit the effectiveness of restoration efforts. Using seismic lines in Alberta’s oil sands as a case study, we demonstrate an approach that integrates spatial configuration of anthropogenic footprints to prioritize habitat defragmentation. We quantified the effects of seismic line density and configuration on functional footprints for caribou, butterfly diversity, and vascular plant diversity, to predict whether edge effects are more pronounced under different line densities and configurations. We then estimated the portion of the original functional footprint that would persist in the landscape due to the co-occurrence with other anthropogenic activities. We found that functional footprint for caribou grows rapidly as habitat loss increases. In contrast, butterflies and plants exhibited a more gradual and linear growth in functional footprints at more local scales. This effect varies based on configuration of lines, either suppressing or facilitating the effect of habitat loss on functional habitats. Finally, restoration of all seismic lines without considering other footprints would reduce the original functional footprint by only 57% for caribou. Restoration efforts for habitat defragmentation rarely consider the spatial configuration of linear features, particularly as it relates to the co-occurrence of other footprints that are not being restored. Our functional approach to defragmentation of habitat encompasses different spatial concepts related to anthropogenic forest fragmentation and allows up to a 25-fold gain in cost-effectiveness for seismic lines restoration.