Web structure mining in static web contents decreases the accuracy of mined outcomes and affects the quality of decision making activity. By structure mining in web hidden data, the accuracy ratio of mined outcomes can be improved, thus enhancing the reliability and quality of decision making activity. Data Mining is an automated or semi automated exploration and analysis of large volume of data in order to reveal meaningful patterns. The term web mining is the discovery and analysis of useful information from World Wide Web that helps web search engines to find high quality web pages and enhances web click stream analysis. One branch of web mining is web structure mining. The goal of which is to generate structural summary about the Web site and Web pages. Web structure mining tries to discover the link structure of the hyperlinks at the inter-document level. In recent years, Web link structure mining has been widely used to infer important information about Web pages. But a major part of the web is in hidden form, also called Deep Web or Hidden Web that refers to documents on the Web that are dynamic and not accessible by general search engines; most search engine spiders can access only publicly index able Web (or the visible Web). Most documents in the hidden Web, including pages hidden behind search forms, specialized databases, and dynamically generated Web pages, are not accessible by general Web mining applications. Dynamic content generation is used in modern web pages and user forms are used to get information from a particular user and stored in a database. The link structure lying in these forms can not be accessed during conventional mining procedures. To access these links, user forms are filled automatically by using a rule based framework which has robust ability to read a web page containing dynamic contents as activeX controls like input boxes, command buttons, combo boxes, etc. After reading these controls dummy values are filled in the available fields and the doGet or doPost methods are automatically executed to acquire the link of next subsequent web page. The accuracy ratio of web page hierarchical structures can phenomenally be improved by including these hidden web pages in the process of Web structure mining. The designed system framework is adequately strong to process the dynamic Web pages along with static ones.