A major hurdle facing data intensive grid applications is the appropriate handling of failures that occur in the grid-environment. Implementing the fault-tolerance transparently at the grid-middleware level would make different data intensive applications fault-tolerant without each having to pay a separate cost and reduce the time to grid-based solution for many scientific problems. We analyzed the failures encountered by four real-life production data intensive applications: NCSA image processing pipeline, WCER video processing pipeline, US-CMS pipeline and BMRB BLAST pipeline. Taking the result of the analysis into account, we have designed and implemented Phoenix, a transparent middleware-level fault-tolerance layer that detects failures early, classifies failures into transient and permanent and appropriately handles the transient failures. We applied our fault-tolerance layer to a prototype of the NCSA image processing pipeline and considerably improved the failure handling and report on the insights gained in the process.