Clinical documents are vital resources for radiologists when they have to consult or refer while studying similar cases. In large healthcare facilities where millions of reports are generated, searching for relevant documents is quite challenging. With abundant interchangeable words in clinical domain, understanding the semantics of the words in the clinical documents is vital to improve the search results. This paper details an end to end semantic search application to address the large scale information retrieval problem of clinical reports. The paper specifically focuses on the challenge of identifying semantics in the clinical reports to facilitate search at semantic level. The semantic search works by mapping the documents into the concept space and the search is performed in the concept space. A unique approach of framing the concept mapping problem as a language translation problem is proposed in this paper. The concept mapper is modelled using the Neural machine translation model (NMT) based on encoder-decoder with attention architecture. The regular expression based concept mapper takes approximately 3 seconds to extract UMLS concepts from a single document, where as the trained NMT does the same in approximately 30 milliseconds. NMT based model further enables incorporation of negation detection to identify whether a concept is negated or not, facilitating search for negated queries.