Freight rail transport plays key role in the transition to sustainable development. However, on European mainlines, freight trains have to cope with busy passenger operation—mostly in the form of (integrated) periodic timetables. Freight trains are characterized with very diverse parameters, so scheduling pre-arranged periodic freight train paths (PFTPs) on the basis of one sample freight train does not meet the needs of most freight operators. This article introduces new detailed framework process for hierarchized construction of differentiated (segmented) pre-arranged PFTPs. The process considers fluctuations in demand for capacity from freight rail operators, so the quality of a freight train path in terms of number of stops is related with its construction priority. This way, the process enhances competitiveness and decreases energy consumption of freight railway, as a factor for sustainable development. Correctness of the framework process is tested on the example of the Prague—Dresden mainline, in the context of prospective (denser) model passenger timetable. Results show that above 70% of real freight trains from the available historical data can fit into the proposed PFTPs. As a conclusion, the authors recommend reduction of service of the least frequent stops of regional trains to reduce number of scheduled stops for freight trains.