Conventional manufacturing systems like assembly lines cannot handle the constantly changing requirements of a modern-day manufacturer, which are driven by volatile market demands. In a bid to satisfy such requirements, modern manufacturing systems, comprising innumerable cyber-physical systems (CPS), aim to be reconfigurable. CPS implement production processes through an ICT infrastructure networked with sensors and actuators embedded in the shop floor. Reconfigurability, in context of manufacturing systems, must include the entire system of networked components and hence requires a flexible ICT infrastructure. Providing flexible ICT infrastructures, often, comes at the cost of diluted quality of service (QoS) guarantees. This, however, is not an option for manufacturing systems, most of which require strict QoS guarantees to function correctly. To overcome this obstacle, we propose a new software-defined environment (SDE) for reconfigurable manufacturing systems with real-time properties in this paper. Software-defined environment is an emerging technology that provides flexible ICT infrastructures modifiable using software. Our contributions include an SDE-based system architecture for dynamically configuring the underlying infrastructure for a manufacturing system. In particular, we focus on configuring the network for the time-sensitive communication flows essential for realising CPS. Moreover, we propose a pair of routing algorithms to calculate routes for these flows while configuring the network.