The main challenges that modern organizations are facing in developing countries nowadays with regards to implementing the e-commerce applications are the factors that affect the level of usability and security of ecommerce applications. Attracting online consumers to purchase online through e-commerce applications is not an easy task and many organizations in developing countries like Libya are facing obstacles to get advantages from ecommerce applications and enhance the trust of customers in order to increase online sales through the development of usability of e-commerce applications installed in their websites. The study will discuss the technical problems associated with implementing and maintaining the high usable e-commerce applications for successful business online, and will evaluate the best solutions to overcome the obstacles that prevent the development of e-commerce applications with high quality and security. This study will contribute to the literatures through developing secure e-commerce applications framework featured with high usability, trustworthy and security that enhance online consumer perception to buy product online with full confidence. The technical security issues will be discussed in terms of providing secure online payment mechanisms for e-commerce application, and discuss the importance of secure payment mechanisms from customer perceptions.