also i have a doubt on microcontrollers.will i be able to run 2 programs simultaneously.i have to keep the stepper motor program running continuosly but when the target is received i will have to run the target recognition program.
As stated by Patrick stated you can but remember that a stepper motor is a critical little bugger as far as pulse spacing.
Some ways to handle it:
a)Use a processor with a PCA or CGA so the stepper motor runs with no program intervention except for speed change. That way you can read barcodes without upsetting the steps.
b) Separate the 2 functions into 2 dirt cheap processors such as a LPC.

Erik