A fundamental challenge in networked systems is detection and removal of suspected malicious nodes. In reality, detection is always imperfect, and the decision about which potentially malicious nodes to remove must trade off false positives (erroneously removing benign nodes) and false negatives (mistakenly failing to remove malicious nodes). However, in network settings this conventional tradeoff must now account for node connectivity. In particular, malicious nodes may exert malicious influence, so that mistakenly leaving some of these in the network may cause damage to spread. On the other hand, removing benign nodes causes direct harm to these, and indirect harm to their benign neighbors who would wish to communicate with them. We formalize the problem of removing potentially malicious nodes from a network under uncertainty through an objective that takes connectivity into account. We show that optimally solving the resulting problem is NP-Hard. We then propose a tractable solution approach based on a convex relaxation of the objective. Finally, we experimentally demonstrate that our approach significantly outperforms both a simple baseline that ignores network structure, as well as a state-of-the-art approach for a related problem, on both synthetic and real-world datasets.