how to fast transition from one line to next ?

hello dear forum,

I am trying to write a G code interpreter for my own motion control hardware ( photo below )

www22.brinkster.com/anotherbrick/index15.htm

I can calculate trapezoidal speed profile for the individual axis
however my code waits to finish each speed profile
until the axis is in 10 micron near to the target point

this in turn makes the motion of the axis stop and go , stop and go for each G code line ( decelaration and acceleration of the axis )
( if you think each G code program is made up from 100s of lines )
however I watched real CNC machines working - they pass from one line to the next very smoothly
they dont stop and go like mine
how can I make my own program same like real CNC machines ?
sorry this is my best english I hope you understood what I mean

thank you