How to fill in the blank cells without scrolling in excel after applying filter.

I wish you provided some sample data to be able to help you precisely.
But here is a general answer:
On the Home Tab ►Click on Find and Select ► Go To Special 
In the dialog box select Blanks ► Hit OK
Start typing without any further clicking
When done ► Hit CTRL + Enter
Hope that helps

Could you please share your dataset sample? If your goal is to fill only the blank cells with a specific formula, you can easily do this by selecting your data range, then pressing F5, clicking Special, and selecting Blanks. Once the blank cells are highlighted, press F2, type your formula, and then press Ctrl + Enter to apply it across all selected blank cells simultaneously.