Yes. First off, you'll need one column of data in your filtered range that
does not contain any blanks. Second, you'll need to add a "helper" column
and fill it with this formula:
=SUBTOTAL(103,$A$2:A2)
This assumes that Column A starts at A2 (A1 being your header) and does not
contain any blank values.
Now, apply Conditional Formatting using this custom formula.
=MOD($D2,2)=0
This assumes that Column D is your newly inserted "helper" column and again,
starts at D2.
Set your formatting, and voila, the alternate shading should be applied
correctly regarless of your filter.
(Note: if you have an older version of Excel, this may not work, as the
SUBTOTAL function was changed in more recent versions.)
HTH,
Elkar