The aim of this paper is to clearly define the chemical and nuclear principles governing Fission Track Analysis (FTA) to determine environmental levels of 239pu in urine. The paper also addresses deficiencies in FTA methodology and introduces improvements to make FTA a more reliable research tool. Our refined methodology, described herein, includes a chemically-induced precipitation phase, followed by anion exchange chromatography and employs a chemical tracer, 236pu. We have been able to establish an inverse correlation between Pu recovery and sample volume and our data confirms that increases in sample volume do not result in higher accuracy or lower detection limits. We conclude that in subsequent studies, samples should be limited to approximately two liters. The Pu detection limit for a sample of this volume is 2.8 p~Bq/1.