Botnets compose a major source of malicious activity over a network and their early identification and detection is considered as a top priority by security experts. The majority of botmasters rely heavily on a scan procedure in order to detect vulnerable hosts and establish their botnets via a command and control (C&C) server. In this paper we examine the statistical characteristics of the scan process invoked by the Mariposa and Zeus botnets and demonstrate the applicability of conditional entropy as a robust metric for profiling it using real pre-captured operational data. Our analysis conducted on real datasets demonstrates that the distributional behaviour of conditional entropy for Mariposa and Zeus-related scan flows differs significantly from flows manifested by the commonly used NMAP scans. In contrast with the typically used by attackers Stealth and Connect NMAP scans, we show that consecutive scanning flows initiated by the C&C servers of the examined botnets exhibit a high dependency between themselves in regards of their conditional entropy. Thus, we argue that the observation of such scan flows under our proposed scheme can sufficiently aid network security experts towards the adequate profiling and early identification of botnet activity.