Yes!! you can partition your pen drive. I will show you how to partition pen drive in real quick easy way. First, download the EASUS partition manager home edition which is free. This software allows you to format, partition, convert, merge the partition of the disk. You can download it from here www.partition-tool.com/personal.htm. After downloading it install to your PC.
How to Partition Pen Drive
Before opening the program insert a USB stick into the USB port. Then open Partition Manager by double clicking the icon on the desktop. The Welcome page appears, click go to main screen. The screen looks like this.
In this picture you can see that there are two disks, Disk1 and Disk2. Disk1 is the hard disk and Disk2 is the USB stick. You can see that Desk2 is Unallocated. This is because I have deleted the existing partition of the stick. We will now create partition on Disk2. So let’s get started.
Right click in the DIsk2′s unallocated are and select create partition. The image below shows how to do this.
After clicking create partition, new box appears similar to below figure. Now type the Label name. Define the size for the partition in Decide size and position section. Then click OK.
Now repeat the previous step to create another partition for remaining unallocated space. Note that you can’t see both partitions in windows explorer because Windows only recognizes first partition on a removable device. If you want to see the other partition, change it to primary partition and give a drive letter. Note: You can see only one partition at a time. If you browse the USB drive with more than one partition in Linux systems, you will see all the partitions. Windows doesn’t support both partitions. You can now use the USB as per your need.