Replace System()call in windows to avoid flickers?

Problem
In My application many times i used system() call like

system(command); to run JAR and DOS related commands.

but whenever i starts my application..many blank pop ups or
flickering(command prompts) comes out (which shows it is executing
system call )

is der any other command which avoids such pop ups ....so that while
running an application it will run smoothly without any flickers ?

thanks you for your valuable time .
Amit