This paper describes a recognition system for online handwritten Tibetan characters using advanced techniques in character recognition. To eliminate noise points of handwriting trajectories, we introduce a de-noising approach by using dilation, erosion, thinning operators of mathematical morphology. Selecting appropriate structuring elements, we can clear up large amounts of noises in the glyphs of the character. To enhance the recognition performance, we adopt a three-stage classification strategy, where the top rank output classes by the baseline classifier are re-classified by similarcharacter discrimination classifier. Experiments have been carried out on two databases MRG-OHTC and IIP-OHTC. Test results show the used recognition algorithm is effective and can be applied to pen-based mobile devices.