Abstract. Field-aligned currents (FACs) in the magnetosphere-ionosphere (M-I) system exhibit a range of spatial and temporal scales that are linked to key dynamic coupling processes. To disentangle the scale dependence in magnetic field signatures of auroral FACs and to characterize their geometry and orientation, Bunescu et al. (2015) introduced the multi-scale FAC analyzer framework based on minimum variance analysis (MVA) of magnetic time series segments. In the present report this approach is carried further to include in the analysis framework a FAC density scalogram, i.e., a multiscale representation of the FAC density time series. The new technique is validated and illustrated using synthetic data consisting of overlapping sheets of FACs at different scales. The method is applied to Swarm data showing both large-scale and quiet aurora as well as mesoscale FAC structures observed during more disturbed conditions. We show both planar and non-planar FAC structures as well as uniform and non-uniform FAC density structures. For both, synthetic and Swarm data, the multiscale analysis is applied by two scale sampling schemes, namely the linear, and the logarithmic scanning of the FACs scale domain. The scale integrated FAC density is computed by both small-scale and large-scale weighting. The integrated multiscale FAC density is compared with the input FAC density for the synthetic data, whereas for the Swarm data we cross-check the results with well established single- and dual-spacecraft techniques. The entire multiscale information provides a new visualization tool for the complex FAC signatures, that complement other FAC analysis tools.