Thank you for reply.

What we have done currently is that,

While creating Finish Purchase order we have added another line item "Exclude Raw Material" which we created as "Service" in product listing. We have checked this service as "I purchase this product/service from a vendor" and have set an expense account called as "Exclude Raw Material". In Purchase order we have set the amount in negative for it. This leads to the total payment to vendor is only the manufacturing cost. So what we have done is right or we need to make any modification. 

I was also looking for something called as "Vendor credit". Can Vendor credit be better solution to this problem. 
I have very less knowledge of Accounting. So i don't know where and what thing go. Any help would be helpful.