is this sentence correct : "I had contacted you for the post of articleship but I had not done with my orientation course but now I am done with it."

Absolutely this is wrong statement. Past perfect is used to express an earlier action of two consecutive actions. Here we have three actions. Moreover the final clause is in the present simple. A perfect and simple tense never be used together. I contacted you for the post of articleship(secondary action) but I hadn't done with my orientation course (primary /earlier action) but I've done with it.(perfect present result)