Can I use an another Atmel microcontroller like SAM3N4 with QFP48 or 64 for devellop with Arduino?
Google cookie arduino.
It uses a NuMicro CM3 chip and is aruidno pin-compatible. All for less than $30.
Having said that, a better choice in my view might be ST F4 discovery, TI LM4F launchpad or KL25 from Freescale. They are not pin-compatible to Arduino but you can easily make an adaptor of your own to do that. They cost $10 - 20 each and come with onboard software / hardware emulator / programmer.
Cookie has a library of its own + free ide.