Hello. Maybe you should try some evolutionary algorithm like Ant Colony Optimization. I found an article concerning your problem:

http://www.academia.edu/1050195/An_Ant_Colony_System_for_Routing_in_PCB_Holes_Drilling_Process

I'm not aware of the context of your question, but Any good CAM software automatically search for the shortest machining operation. There are however some algoritms you could use to get the shortest path between multiple points,such as this one : http://www.codeproject.com/Articles/22647/Dijkstra-Shortest-Route-Calculation-Object-Oriente

Thanks Marco

Will you please suggest me some of the PCB/CAM software which will solve my problem.

Nearly everyone CAM software has an option to optimize the move tool. Such as NX

Dear Daniel

Ya I am trying to do it with EAGLE.

It is essentially an optimizing problem of minimizing the distance traveled. Many approaches were tried. here I found some references for you.

Onwubolu, G. C., & Clerc, M. (2004). Optimal path for automated drilling operations by a new heuristic approach using particle swarm optimization.International Journal of Production Research, 42(3), 473-491.

Magirou, V. F. (1986). The efficient drilling of printed circuit boards. Interfaces,16(4), 13-23.

Lim, W. C. E., Kanagaraj, G., & Ponnambalam, S. G. (2012). Cuckoo search algorithm for optimization of sequence in pcb holes drilling process. In Emerging trends in science, engineering and technology (pp. 207-216). Springer India.

Onwubolu, G. C. (2004). Optimizing CNC drilling machine operations: traveling salesman problem-differential evolution approach. In New optimization techniques in engineering (pp. 537-565). Springer

Berlin Heidelberg. Adam, A., Abidin, A. F. Z., Ibrahim, Z., Husain, A. R., Yusof, Z. M., & Ibrahim, I. (2010, May). A Particle Swarm Optimization Approach to Robotic Drill Route Optimization. In Mathematical/Analytical Modelling and Computer Simulation (AMS), 2010 Fourth Asia International Conference on (pp. 60-64). IEEE.