We have been working on mercury collection from flue gas by amalgamation and subsequent XRF analysis. Previous results showed unexpectedly high relative standard deviation (30%) in collection efficiency when silver-coated filters were exposed to gas phase mercury in a pilot-scale test chamber. Filters were analyzed by micro-XRF, TXRF and conventional XRF to explore the source of scattering. It was concluded that mercury had inhomogeneously adsorbed in the filter as the cause of this variation, leading to a positive bias of 50% in efficiency value. Results reported in this paper suggest the TXRF method is accurate to within ±10% when X-ray counting statistics are not the limiting factor. Application of this filter in flue gas measurement will be presented.