Currently, Cytobank does not support the deletion of FCS files from an experiment.
There are, however, two workarounds to otherwise remove FCS files from your analysis.
1. Selectively Clone the Experiment and remove the unwanted file(s).
2. Categorize the file as a Compensation Control within your experiment. This is a quick workaround and removes it from most pages in the Experiment and makes the file not part of analyis outside the compensation page.