In ISIS (and other amateur packages) this is usually taken account for in the single combined step for instrument and atmospheric response correction.
The approach is take a spectrum of a standard A or B type star that has a spectrum in the Miles or similar database, and that it is at a similar altitude to your target. You use your spectrum along with the one from the Miles database to calculate a combined instrumental and atmospheric response correction. Where this won’t work is if you try to observe a target at a significantly different altitude, or if the sky conditions change. In that case you would need to take a fresh spectrum of an appropriate A or B type star.
When removing individual atmospheric telluric lines then it will be necessary to take a more sophisticated approach. ISIS has another tool which can be used for that but often this step is not needed for the target spectra. I also find this only approximately works rather than giving a really good telluric removal.