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I have a feature class of land parcels. I do a select by location to select the land parcels that intersect a line feature. Now I want to use the Make Query Table tool in model builder. I include the Shape field to ensure my output is still a feature class however the table is created with all the data and not just the selected features. How do I run a make query table on a selection and not the whole feature class?

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It's late, I'm not thinking terribly straight, and I haven't done this in several months, but it sounds like you need to add a Make Feature Layer step between your SQL query and your Make Query Table in the model. Your selection output is the input for the Make Feature Layer and the output of that is your input for the Make Query Table. Tools in Modelbuilder run on layers, not the feature classes behind them, so your selection is made and then dismissed as the data is passed to the next step - you have to output the results of the selection to a layer to actually do something with them. Said layer is temporary and not saved unless you configure it to be in the MFL tool, which can be useful for testing and then turned off for final 'publication'.

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