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A new multi-spectral laser radar (ladar) system based on the time-correlated single photon counting, time-of-flight technique has been designed to detect and characterise distributed targets at ranges of several kilometres. The system uses six separated laser channels in the visible and near infrared part of the electromagnetic spectrum. The authors present a method to detect the numbers, positions, heights and shape parameters of returns from this system, used for range profiling and target classification. The algorithm has two principal stages: non-parametric bump hunting based on an analysis of the smoothed derivatives of the photon count histogram in scale space, and maximum likelihood estimation using Poisson statistics. The approach is demonstrated on simulated and real data from a multi-spectral ladar system, showing that the return parameters can be estimated to a high degree of accuracy.