Commercial invoice for manufacturer

You can send the material along with the original invoice.  You need not pay any excise duty on that.

Excise duty is not payable on removal of inputs on which cenvat credit is not availed, 

no entry needed in any excise records, as the same is neither entered in RG23A-Part1 or Par4t 2 at the time of purchase. 

Any form 4 register will made for it

when the inputs are not recorded in excise records, at the time of clearance, you dont have to record for excise, but in your own stock register, you have to record it , as inward and outward entry.