This research is motivated by a deterministic scheduling problem that is fairly common in manufacturing environments, where there are certain processes that call for a machine working on multiple jobs at the same time. An example of such an environment is wafer fabrication in the semiconductor industry where some stages can be modeled as batch processes. There has been significant work done in the past in the field of a single stage of parallel machines which process jobs in batches. The primary motivation behind this research is to extend the research done in this area to a two-stage flow-shop where jobs arrive with unequal ready times and belong to incompatible job families with the goal of minimizing total weighted tardiness. As a first step to propose solutions, a mixed integer mathematical model is developed which tackles the problem at hand. The problem is NP-hard and thus the developed mathematical program can only solve problem instances of smaller sizes in a reasonable amount of time. The next step is to build heuristics which can provide feasible solutions in polynomial time for larger problem instances. The basic nature of the heuristics proposed is time window decomposition, where jobs within a moving time frame are considered for batching each time a machine becomes available on either stage. The Apparent Tardiness Cost (ATC) rule is used to build batches, and is modified to calculate ATC indices on a batch as well as a job level. An improvisation to the above heuristic is proposed, where the heuristic is run iteratively, each time assigning start times of jobs on the second stage as due dates for the jobs on the first stage. The underlying logic behind the iterative approach is to improve the way due dates are estimated for the first stage based on assigned due dates for jobs in the second stage. An important study carried out as part of this research is to analyze the bottleneck stage in terms of its location and how it affects the performance measure. Extensive experimentation is carried out to test how the quality of the solution varies when input parameters are varied between high and low values.