Solution
Change the Default Application and Device control policy and allow the specific drive.
For Example, To change the policy in order to allow the secondary hard drive :
1. Logon to SEPM and Click on Policies
2. Edit the Default or modified Application and Device Control Policy (Whichever applied to the group where you want to allow secondary hard drives)
3. Select Application Control and highlight Block Access to Autorun.inf[AC9] and Click on Edit Button
4. Under Rules highlight [AC9-1.1]Autorun.inf
5. In Properties pane under "Apply to following files and folders" box highlight *\Autorun.inf (enable drive types) and click on Edit button
6. From Edit File or Folder Definition Box locate Option list for Only match files on the following drive types
7. Uncheck the specific drive you want to install on the machine (E.g. : Local Fixed Disk Drive )
8. Click on OK and Assign the policy to the group containing secondary drives