First, you need to enable the admin API via the command line:

--web.enable-admin-api

Now you can delete a metric by calling the respective endpoint, for example by using curl.

curl -v -X POST -g 'http://localhost:9090/api/v1/admin/tsdb/delete_series?match[]=node_cpu_seconds_total'

This will delete all timeseries called node_cpu_seconds_total.

The actual data still exists on disk and is cleaned up in future compactions or can be explicitly cleaned up by calling the clean_tombstones endpoint:

curl -X POST http://localhost:9090/api/v1/admin/tsdb/clean_tombstones

See the official Prometheus docs for more useful admin API endpoints.