A method of analyzing a target item utilizing multiple scanners, comprising: providing an item comprising a material; acquiring a first set of scan data associated with said item using a first, three-dimensional computed tomography scanner; acquiring a second set of scan data associated with said item using a second, multi-energy line scanner, the second set of scan data comprising a two-dimensional projection image of effective atomic number data, or electron density data; generating a first set of transform data from said first set of scan data, the first set of transform data comprising absorption coefficient data; analyzing said first set of transform data to identify a subset of said first set of transform data associated with a first region; analyzing said second set of scan data to identify a subset of said second set of scan data associated with a second region; and generating a measure that at least a portion of scan data is consistent with a presence of a candidate material in said item, where said portion of scan data is selected from at least one of the set consisting of: said subset of said first set of transform data and said subset of said second set of scan data; the method further characterized by: mapping the first and second regions onto a two-dimensional image, determining one or more areas covered by the first and/or second regions on the two-dimensional image, and analyzing the one or more areas to identify the presence of the candidate material; wherein: for areas where the mapped first region overlaps with the mapped second region, candidate materials are identified by analyzing both the first set of transform data and the second set of scan data; for areas that are mapped within the first region but outside the second region, candidate materials are identified by analyzing the first set of transform data only; and for areas that are mapped within the second region but outside the first region, candidate materials are identified by analyzing the second set of scan data only. providing an item comprising a material; acquiring a first set of scan data associated with said item using a first, three-dimensional computed tomography scanner; acquiring a second set of scan data associated with said item using a second, multi-energy line scanner, the second set of scan data comprising a two-dimensional projection image of effective atomic number data, or electron density data; generating a first set of transform data from said first set of scan data, the first set of transform data comprising absorption coefficient data; analyzing said first set of transform data to identify a subset of said first set of transform data associated with a first region; analyzing said second set of scan data to identify a subset of said second set of scan data associated with a second region; and generating a measure that at least a portion of scan data is consistent with a presence of a candidate material in said item, where said portion of scan data is selected from at least one of the set consisting of: said subset of said first set of transform data and said subset of said second set of scan data; mapping the first and second regions onto a two-dimensional image, determining one or more areas covered by the first and/or second regions on the two-dimensional image, and analyzing the one or more areas to identify the presence of the candidate material; wherein: for areas where the mapped first region overlaps with the mapped second region, candidate materials are identified by analyzing both the first set of transform data and the second set of scan data; for areas that are mapped within the first region but outside the second region, candidate materials are identified by analyzing the first set of transform data only; and for areas that are mapped within the second region but outside the first region, candidate materials are identified by analyzing the second set of scan data only. for areas where the mapped first region overlaps with the mapped second region, candidate materials are identified by analyzing both the first set of transform data and the second set of scan data; for areas that are mapped within the first region but outside the second region, candidate materials are identified by analyzing the first set of transform data only; and for areas that are mapped within the second region but outside the first region, candidate materials are identified by analyzing the second set of scan data only.