The layered architecture pattern has been widely adopted by the developer community in order to build large software systems. The layered organization of software modules offers a number of benefits such as reusability, changeability and portability to those who are involved in the development and maintenance of such software systems. But in reality as the system evolves over time, rarely does the actual source code of the system conform to the conceptual horizontal layering of modules. This in turn results in a significant degradation of system maintainability. In order to re-factor such a system to improve its maintainability, it is very important to discover, analyze and measure violations of layered architecture pattern. In this paper we propose a technique to discover such violations in the source code and quantitatively measure the amount of non-conformance to the conceptual layering. The proposed approach evaluates the extent to which the module dependencies across layers violate the layered architecture pattern. In order to evaluate the accuracy of our approach, we have applied this technique to discover and analyze such violations to a set of open source applications and a proprietary business application by taking the help of domain experts wherever possible.