Screening and development of industrial process for enzymatic delignification is an option for those industries who want to minimize acids and chlorine containing bleaches, thus minimizing the impact on environment. For commercial applications, it is important to screen fungi producing lignin modifying enzymes (LMEs) and adapting them to industrial media for submerged fermentations. Using functional plate assays and a full factorial design (FFD) approach, an optimal media composition for the highest expression of these LMEs has been achieved in this study. Two fungal strains (Trametes versicolor and Pleurotus ostreatus) were selected for evaluation. SDS PAGE and native gel analysis confirmed the results of screening and submerged culture media optimizations. When rice straw was added as inducer, secretion of additional enzymes other than laccases such as manganese peroxidase (MnP), lignin peroxidases (LiP), and versatile peroxidase (VP) in the cultures has been observed. This paper also demonstrates an improved process of enzymatic pretreatment resulting from a washing step introduced before saccharification (Scheme. 1). Hence, the current study proposes that removal of LMEs by washing helps in improvement of cellulase/hemicellulose depolymerization efficiency.