A Traceability Matrix can be easily created using a spreadsheet, but also specialized software is avaiiable.
Create a spreadsheet with a row for each requirement. Put the requirement number in the first column, followed by the requirement description, the GMP relevance and the Risk Priority (from the Risk Assessment). Create columns for each document that will be created, like Functional Specification, Software designs and Test Specifications (pre-FAT, FAT, SAT, IQ, OQ, PQ). When a document is release, fill the column for that document with a reference for the requirements. When requirements are not referenced in the document, the requirement could be forgotten. Indicate the reference with 'Not Applicable' when the requirement is not intended to be described in that document. At the end of the project al columns should be filled. Conclusions may be referenced in the Validation Summary Report.
The above picture shows a small screenshot of a Traceability Matrix.