A method of identifying a software vulnerability in computer systems in a computer network includes a multiple level scanning process controlled from a management system connected to the network. The management system runs a root scanner which applies an interrogation program to remote systems having network addresses in a predefined address range. When a software vulnerability is detected, the interrogation program causes the respective remote system to scan topologically local systems, the remote system itself applying a second interrogation program to the local systems to detect and mitigate the vulnerability using an associated mitigation payload. Whilst that local scanning process is in progress, the root scanner can be applied to remote systems in other predefined address ranges.