I've Motorola Symbol Handheld Model MC3090 (from symbol MC3000 series), having Windows CE 5.0.
Is it possible that i can upgrade the Handheld OS from CE 5.0 to CE 6.0?
In Short - NO.
To be able to do so you need to have the BSP (board support package) to build an image for Windows CE. Each OS is built specifically for each device. When you say Windows CE 6 it means nothing since it is a componentizied OS and your OEM (Motorola) decides what to put inside.
According to device's specs I think it has Windows Mobile. A different beast than Windows CE, but based on Windows CE 5. There is no Windows Mobile based on Windows CE 6.
In any case you cannot change the OS version without the OEM.