Critical infrastructures play a central role in the welfare of contemporary societies and they should properly function 24/7. Since their role is so important, they regularly become targets of malicious parties, terrorists, industrial spies, and even hostile governments. In this paper, the scenario of cyber or physical attacks to CIs from tiny autonomous malicious drones is analyzed. In particular, this work focuses on indoor spaces, protected by mini-drones. The mini-drones are equipped with harmonic radar and run a novel algorithm, which guides them to scan the whole area. Assuming that the malicious drones behave as non-linear systems, the mini-drones transmit signals and analyze the received signals, creating a non-linear system 3D location map for the whole space. In the consecutive scans, any changes on the 3D location map indicate that the malicious drone has changed location. Simulated results and comparisons to state-of-the-art approaches exhibit the cost-effectiveness and time efficiency of the proposed scheme as well as its limitations.