Disclosed are a system and method for processing HL7 messages. A method includes receiving, an HL7 message; storing the HL7 message in a memory; creating a data structure representation of the stored HL7 message in the memory that stores a start index and an end index of the stored HL7 message, wherein the start index indicates a beginning of the stored HL7 message and the end index indicates an end of the stored HL7 message; hierarchically creating, from the data structure representation of the stored HL7 message, one or more data structure representations in the memory that store at least one start index and at least one end index corresponding to one or more fragments in the stored HL7 message; and, modifying the stored HL7 message according to the at least one start index and a corresponding end index of the fragments in the HL7 message.