The demand for customized products in a saturated market of trendy customers forces the manufacturing industries to transform their manufacturing from a high volume of uniformed products to low volumes and a high mix of products. High mix and low volume manufacturing is most often manually performed since existing automation solutions are only profitable for mass manufacturing, due to explicitly designed control software where the product data is implemented as low-level control code. Highly flexible automated manufacturing systems such as Plug & Produce are requested, but challenges still exist before industrial implementation. This article proposes a digitally configurable system where data for new or modified products data is configured from the perspective of the product and its manufacturing processes instead of the manufacturing resources. In a Plug & Produce system, process modules with manufacturing resources are easy to replace for new or modified products and possibly to duplicate if higher capacity is needed. Configurable multi-agent systems are proposed by several researchers as a control system for Plug & Produce. An agent is a piece of autonomous computer code that negotiates with other agents and concurrently solves tasks, distributed on parts and resources. A part is a part of a product and part agents handle manufacturing goals for the parts. Resource agents know their capability and start operating as soon as they are plugged in. Resource agents follow pluggable process modules containing manufacturing resources and act as drivers for the modules. Gantry robots have by design a naturally orthogonal coordinate system and most often lack the functionality to handle work and tool coordinate objects as standard industrial robots do. Work objects refer to a base coordinate system and tool objects contain a reference to the tool center point. These references are in this article integrated into resource agents together. A place coordinate agent has the global perspective of the Plug & Produce cell and provides the process modules with reference coordinates of the place they are plugged into. Coordinates are recalculated from a product perspective into a resource perspective by coordinate transformations built into the skills of resource agents. This structure enables the possibility for process planners in the manufacturing company to make changes on a daily basis. A test with a gantry robot Plug & Produce demonstrator was performed and presented in this article to verify the generic structure of the gantry robot control system into agents.