Since you worded it as "if I copy the entire iso file to the pen drive" I want to just clarify something. You do not want to copy the .iso file to the thumb drive. You need to use an utility, such as UltraISO, to extract the ISO contents first. It is those files that need to be on the thumb drive. Also make sure that whatever is in the root of the ISO is also in the root of the thumb drive. I have seen people copy the ISO contents into a folder on the thumb drive and then be surprised why it won't boot.
"if this is a windows installation disc image, mount the ISO (e.g. with WinCDEmu) then use WinToFlash to create a bootable USB stick. it doesn't get any easier.
Can my system boot through pend drive?
unless you post make and model of your system, this is hard to answer, but most modern computers can boot from USB. :)"