Cellulose based nanofilms have large applications in biomedical and related fields due to their antimicrobial properties. Their applicability depends upon purity of cellulose, composition, and structural properties of films. The nanofilms of cellulose extracted from Water Hyacinth (Eichhornia crassipes) and Roselle (Hibiscus Sabdariffa) plant possesses excellent properties for biomedical applications due to their biological origin and ZnO or other metal loading properties. Microwave assisted physical separation of cellulose provided excellent films formation properties and ZnO loading compared without any chemical traces. The presence of chemical impurities to affects structural, morphological properties and contact angle. It affects the biomedical applicability of cellulose based films. The microwave-based extraction was further assisted by use of polyethylene glycol with molecular weight 600, which increases the solubility and extractability of cellulose to 90 %. Formed films showed higher contact angle and hydrophobicity. This increased hydrophobicity of cellulosic nanofilms showed enhanced antimicrobial activities towards gram-negative and gram-positive bacteria by water hyacinth nanofilms. Thus, microwave-based synthesis of cellulose nanofilms resulted into enhanced microbial activities.