In this paper, modeling of ANFP (active nano fountain pen) and a nano size line control system with ANFP based on fuzzy algorithm is developed. It was found that line width is affected directly with initial mass of meniscus; velocity of patterning and concentration of ink directly affect line width. The control algorithm using the result of modeling successfully shows that the speed of patterning is increased and a variation of line width is possible compared with DPN (dip pen nano lithograph) and FPN (fountain pen nano lithograph). The control of line width system with ANFP is developed by using fuzzy algorithm. Finally, it is shown that it is possible to develop an effective control of variant line width with the same speed.