I have run into this problem before too. Most operations
(copy,fill,find,replace,goto etc.) only use the visible cells, paste is an
exception to the rule.

One possibility is to copy a unique ID column from the filtered data and
paste to the left of the figures you have changed. Then you can fill down a
vlookup formula to update the column with the changed figures. (To create the
ID column you could fill down in an adjacent column =ROW()). Don't forget to
remove the filter and paste values after though.

A cleaner method is to insert a new column in the filtered data and use
Edit>Fill>Right make the updates and then Edit>Fill>Left after.

Other spreadsheet programs or other excel files???

I'm not quite sure what you're doing, but sometimes you can sort your data to
group what you want so that there are no hidden cells in the area you want to
paste.

Or maybe you could show all the rows, then copy that column and apply a filter
to show just what you need.

Then make your changes and show all the data and paste the entire column over
the original data.