If it is a pattern from a pattern swatch in the Swatches panel, you could try this:
Select the background filled with the pattern and use Object > Expand... > Fill
Ungroup the result and choose Object > Clipping Mask > Release
Select a no fill /no stroke object and choose Select > Same > Fill & Stroke
Delete the selection.
Select the expanded pattern and choose Object > Live Paint > Make
Use the Live Paint bucket (K) to fill area's