If you can't stain the cultured cells IN the wells (then observing by LM) you might find perhaps some solution in the following threads I found on RG: 

https://www.researchgate.net/post/Is_there_a_protocol_for_lysis_of_endothelial_cells_grown_on_on_24well_transwell_filters

 https://www.researchgate.net/post/How_to_isolate_pick_single_cells_in_order_to_make_a_isogenic_cell_line

 https://www.researchgate.net/post/I_am_scraping_bacterial_films_from_96_well_plates_Is_there_anything_to_make_this_easier_Special_scrapers_coatings_or_inserts2

 https://www.researchgate.net/post/How_can_I_remove_spheroids_from_96-well_flat-bottom_plate_with_agarose

 https://www.researchgate.net/post/What_sonication_time_40_KHZ_is_safe_to_recover_viable_bacteria_from_biofilm_formed_in_96-well_plates

 https://www.researchgate.net/post/Is_it_feasible_to_do_cell_viability_test_by_counting_cells_using_trypan_blue_in_a_96-well_plate_How_can_I_detach_cells_from_wells_exactly

 https://www.researchgate.net/post/What_is_the_best_way_to_harvest_adherent_macrophages_out_of_48-well_plates

 Best wisshes and good luck.