help with painting hard top

hi all i have bought a hard top but it is all bubbly on the top under the paint, i have now spent 2 hours sanding them all down but they are still there if i feel the top, i guess the fibreglass roof is the problem, i surely cannot fill the full top with filler is there a easier way!! there is hundreds of them only small now but worried i will go through the top if i keep sanding!! thanks all

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