A thin film deposition system includes a web guide system having a plurality of web guides defining a web transport path for the web of substrate. The web guide system includes a moveable portion including first and second moveable-position web guides. A web transport control system advances the web of substrate along the web transport path at a web advance velocity. A deposition head is located along the web transport path between the first and second moveable-position web guides. A motion actuator system synchronously moves a position of the first and second moveable-position web guides such that they move forward and backward according to a defined oscillating motion pattern while maintaining a constant distance between the first and second moveable-position web guides, thereby causing a portion of the web of media adjacent to the deposition head to move forward and backward in an in-track direction.