In this publication, according to the results of a comparative analysis, a hypothesis is adopted about a faster and less resource-intensive method of search, detection, and control of invasive plant species on the example of control of Sosnowsky’s hogweed by the forces and means of the group operating an unmanned aircraft system (UAS). A typical algorithm for the operation of samples and software models, autonomously operating UAS, consisting of vehicles of different functional purposes, is also proposed. To solve the problem, the specification of the UAS tools used is described. Different echelons of unmanned aerial vehicles for solving tasks and different options of scanning in stripes can be applied. Moreover, three flight trajectories for an unmanned aerial vehicle intended for spraying toxic substances are suggested. The type of take-off and descent is selected based on the terrain data. Finally, the equations of the optimization problem for spraying with the help of UAS are composed depending on the type of the trajectory and the initial data.