I have a 98 honda civic ex 1.6L. It will not start. I thought it was the fuel pump but that is working fine. The fuel filter has also been recently replaced. What could be the problem with it starting?

If the CEL comes on and goes off after 2 seconds, when the ignition switch is turned to ON (Position II), then I would replace the Ignition Control Module (ICM) and coil:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-4.html#post265896

If you prefer, perform tests, in Honda Sections 1 and 2, below:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563.html