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In Sketchup, running the 'OSM Diagnostic Script' (Extensions > OpenStudio User Scripts > Reports > OSM Diagnostic Script) on your model with 'Remove Objects with Warnings?' set to 'true' will remove surfaces with area less than 0.1 m^2. I find this to be a decent quick fix. If you want to change that criteria, you can edit the script, which is located at C:\Program Files\OpenStudio 1.11.4\Ruby\openstudio\sketchup_plugin\user_scripts\Reports
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Avoiding the creation of these surfaces in the first place is tricky, and involves being very careful with how you set up geometry for the building as a whole, not just floor by floor.