It is possible to use Arduino Hardware with AVRStudio i.e. you can write your code in assembly or C Code in AVRStudio and the generated Hex file can be downloaded to your Arduino UNO or Arduino Mega using the bootloader and without the need of any hardware (AVR ISP etc). The details are as given in the following link.
Thanks Nick. But only recently (~2 to 3 years??) avrdude has "arduino" as programmer to assert the hardware (DTR) reset and enter bootloader. Before that it was a trick which I used "mode" command in batch file to workaround.
Just helping guys to explore more with opensource Arduino hardware. Further AVRStudio is an important part for learning Atmel products.