Natural active compounds from plants have an increasing economic meaning in all areas of life sciences like e.go., food additives, cosmetics, pharmaceuticals and crop protection. The main task in manufacturing larger amounts of these plant based products besides raw material supply, product stabilization, and quality assurance, is an efficient process development method and economic production technology. State of the art approach is used in standard extraction methods. Initially their quantities are determined in isolation of laboratory scale testing and then transferred into large-scale production by keeping all operation parameters constant in order to keep product quality constant. Nowadays the problem is that in most cases besides any missing process optimization with regard to necessary economical objectives, equipment is used with no modem process control, automation or process integration design applied. This study is a first proposal for a systematical process development and design methodology. It should address the need for efficient process evaluation of many compounds at an early stage and process optimization for manufacturing. Due to sustainability and economy the maximal yield contained of any target compounds in plants should be extracted, but this increases as well the side component amount and type extracted and thereby decreases product purity. Therefore, any approach to optimization, should be integrated with a process development and evaluation of additional purification steps. This article describes the experimental setup as well as modeling approaches, combined with experimental model parameter determination, to generate the basis for any total process optimization by simulation. As an example the extraction of target compounds from wood is chosen.