This paper addresses the problem of resolving ambiguities in frequently confused online Tamil character pairs by employing script specific algorithms as a post classification step. Robust structural cues and temporal information of the preprocessed character are extensively utilized in the design of these algorithms. The methods are quite robust in automatically extracting the discriminative substrokes of confused characters for further analysis. Experimental validation on the IWFHR Database indicates error rates of less than 3 % for the confused characters. Thus, these post processing steps have a good potential to improve the performance of online Tamil handwritten character recognition.