Abstract: A flexible, modular thin film deposition machine comprises a number of batch process stations which define a batch process path. At least one of the batch process stations is a thin film deposition station including a serial deposition chamber and an inter-chamber disk transfer mechanism. The disks move in batches along the process path, being individually processed only at the deposition station. Within the serial sputtering chambers of at least one deposition station there is at most partial environmental separation, whereas between different deposition stations the separation is complete. The resulting simplification of the transport mechanism provides for a high throughput rate while simultaneously minimizing contamination of individual thin film layers.