Decorticated flax contains a significant amount of shive content, which limits applications of flax fibre. Separation of shives from the fibre is essential to improve the quality of flax fibre. Pneumatic method and a Sorter were implemented to meet the above objective. Terminal velocities of individual flax fibre and shive particles were investigated and their width, length, and mass were recorded. A sorting method was used for separation of short and long fibre for two grades of fibre: Grade 1 and Grade 2, with initial fibre purities of 51% and 15%, respectively. The ranges of terminal velocities for shive and fibre particles were 1.13 to 4.09 m/s and 0.51 to 1.07 m/s, respectively, which were significantly different. Fibre purity of approximately 80% for Grade 1 and 66% for Grade 2 were recorded from sorting, which were a significant improvement when compared to the initial purities. This study demonstrated the potential of the pneumatic and sorting methods for improving fibre quality. With the increase in resistant strains of microorganisms to antibiotics, researchers have started to explore plant parts to discover new antimicrobials. Since medieval times all portions of plants were used medicinally. Plant tissues, including stems, possess secondary metabolites (SMs), which have known antimicrobial properties. The purpose of this study was to investigate: the presence of antimicrobial compounds in stem extracts of canola, flax, hemp, and sweet clover; and study sorption-desorption behavior of their powdered stem material. GC-MS analysis of all extracts showed the presence of many SMs, including fatty acids, terpenoids, steroids, and sterols, etc. Many of the SMs found in the extracts have previously shown antimicrobial activity against a broad spectrum of organisms according to literature. Water sorption isotherms of stems showed a typical IUPAC Type II sigmoid curve similar to natural fibres. Equilibrium moisture content (EMC) of canola and sweet clover was significantly higher than flax and hemp at 95% RH, which were all higher than the fibre saturation point of wood (27%). The preliminary investigation via GC-MS showed promising results and water absorptivity results of stems can be used as the initial key property for many applications.