Biomass is central to carbon-neutral energy systems, yet its heterogeneity and low bulk density hinder efficient conversion. Pre-treatment operations (drying, size reduction, torrefaction, and densification) are essential for stabilizing feedstock properties and enhancing conversion performance. This study examines how these stages are represented in Aspen Plus models and identifies methodological gaps through bibliometric and literature analyses. Performance analysis shows that most Aspen-based studies focus on gasification and pyrolysis, while explicit modelling of pre-treatment remains limited. Examination of thirteen representative papers confirms that biomass is typically assumed to be an already pre-treated input, despite the strong influence of feedstock characteristics on reactor behaviour, energy efficiency, and emissions. Scientific mapping highlights active collaboration among European countries but limited representation from the Baltic region. Three potential improvement scenarios for a Latvian pellet plant demonstrate how Aspen Plus can link feedstock properties with technical and economic performance, supporting the optimization of pelletisation and pre-treatment processes crucial for advancing sustainable bioenergy systems.