Flash memory has gained great popularity for its properties of low latency, high parallelism, energy efficient, and small volume. But the direct substitution of flash-based solid state drives for hard disk drives has hidden these properties from the operating system, preventing the operating system from optimizations. In this paper, comparison and analysis are made on the storage systems built on the raw flash, including flash accelerating cards, flash arrays, and flash-based clusters, which have achieved the goals of low latency, high reliability and energy efficiency through hardware interface change, software or controller module refinement, or computation and I/O capacities matching. Based on the comparison of these recent raw flash based storage systems, challenges and design issues are discussed on three aspects. Firstly, performance optimizations with I/O stack redesign are surveyed from the hardware interface, notification mechanisms, the system software refinement or redesign, and new storage interfaces for rich semantics. Secondly, the reliability approaches from the system level are described. Finally, the energy efficiency and the volume gains from the flash based storage are presented. After the discussion, the research works are summarized and the possible research directions are pointed out.