Yes, you can, and indeed must.
Ich is a protozoan infection, and has three stages to its life cycle. Whilst they are in the white cysts, they are impervious to treatment. Once the cyst come off, the eggs fall off and develop in the substrate, and again are impervious to treatment. Once the eggs hatch, and the protozoa are swimming freely, looking for a host to continue the life cycle, that's when they can be treated.
If you purchase your treatment, it will have treatment instructions on the bottle. Follow them to the letter. It should tell you to keep treating after all the spots have disappeared, and hopefully the above will explain why that is. It may also help to temporarily increase the water temperature, as this speeds up the metabolic rate of the protozoa, meaning they reach the free-swimming stage quicker.