Maintenance activities are necessary to maintain the functionality of the railway infrastructure. Commonly, the maintenance activities are planned first. Then, the timetable is elaborated respecting the unavailability periods caused by the former. However, unplanned maintenance activities may have to be introduced at short notice, and the timetable must be rearranged. In addition, specific trains may be necessary to perform maintenance activities, and they are typically not scheduled in the timetable. In this case, the timetable may need to be further modified to integrate the maintenance trains. In this paper, we propose a mixed integer linear programming formulation that modifies a timetable to cope with maintenance activities. It includes the consideration of maintenance trains and other specific constraints, such as temporary speed limitations. In this formulation, the modified timetable is optimized based on a microscopic representation of both the infrastructure and the rolling stock. We test the proposed formulation on a real case study in the French railway network and we show its practical applicability.