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I want to select and save as a separate shape file, a smaller section (polygon) from a whole island country which includes both land and shallow habitat coastal features (like coral reefs) and when I draw and select a polygon, the indicated yellow selected area includes areas outside of the polygon I have drawn.

What am I doing wrong so that I can select polygons that are subsections of larger maps without including these 'outside' areas?

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Welcome to GIS SE! I am having trouble picturing what you are describing in words so will +1 your question to hopefully give you enough reputation to edit your Question so that it includes a graphic. – PolyGeo Nov 5 '13 at 9:55

Seems your data is using Multipolygons.

Switch the layer to Editing mode , then try Vector -> Geometry Tools -> Multipart to singleparts

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Thanks for the suggestion, but it does not fix the problem unfortunately. Is there a 'Cut' tool in QGIS like in ArcView? – user20992 Nov 6 '13 at 7:55
Actually, just saw there is a cutting tool in the Digitising plugin but I cannot activate it (its in grey mode). How can I make it active? – user20992 Nov 6 '13 at 8:03
To activate the icon, you have to select a feature with the Select features Tool. But this will delete the whole feature. – AndreJ Nov 6 '13 at 8:39

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