How to install windows on Macbook Pro having Apple File System?

Use bootcamp assistant to partition the SSD, then install windows on the new windows-supported partition.

Alternatively boot into recovery mode, use disk utility to delete the existing partition (this will wipe everything, if you have anything you need on the Macbook's SSD back it up first), then install windows and let the windows installer partition the SSD.

If you have already created your bootable Windows 8.1 install USB thumb drive you should be able to just follow the prompts inside the Boot Camp application.

After you create the Windows installer the Mac will reboot and give you a dialog box that allows you to allocate the amount of space you want to dedicate to Windows. Just slide the handle in the middle left or right until you have the desired space configuration.

You should not have to concern yourself with the file system the Mac side is using as Boot Camp will format that part of this disk specifically for windows.