Since the middle of 1990s, Malaysia has already showed its commitment and emphasis on the idea of Information and Communication Technology (ICT). Malaysia's Multimedia Super Corridor (MSC) is being developed in order to satisfy the country's ambition to achieve the fully developed status by the year 2020. Recent studies showed that online learning for secondary students had become more established and accepted as a standard way of learning nowadays. Educators are always being encouraged to incorporate technology into their classroom teaching. 3D interactions with multimedia elements relatively allow the learners to learn and grasp the lessons being taught much faster than in a normal classroom. The use of computer training tools where the student can interact with a computer model can give good feedbacks. 3D analytical approach is especially useful in determining the fundamental molecular events using a Web-based, visually-oriented system that allows efficient querying of gene expression. The implementation of VRML is perceivably efficient and effective method for conveying molecular models over the net. In molecular science, 3D impressions and conceptions are elementary in order to transfer and understand further complex structural information. A prototype of an interactive 3D multimedia learning tool in Biology was created in order to provide users with a 3D element multimedia study environment in Biology subject. The prototype contains three main divisions which are the 3DiC, animations and tutorials. It allows users to learn and study about the biological cells and animations in an interactive and interesting 3D environment.