I am having troubling to get rid of these black regions in my ListContourPlot

Here is the sample data from the one of region form the figure! (Thank you @Corey979 for helping me to find place to share the data)

http://pastebin.com/y6XG4hib

The sample data plot looks like this

• Or to irregular distribution, like missing points. You can check if this effect is present with a subset of your sample (first 1000 points, or every 1000th point, or so), and then upload this smaller sample on, e.g., pastebin.com – corey979 Jan 19 '17 at 18:06
• @corey979 Thank you! I was able to get some part of the image – Saesun Kim Jan 19 '17 at 19:02

Your data has issues, and you need to do some kind of smoothing before you can use ListContourPlot.

data = << "http://pastebin.com/raw/y6XG4hib";
ListPointPlot3D[data]


From there you can see the issue, but it's clearer if you isolate one of those lines,

GatherBy[data, First] // ReplaceAll[{x_, y_, z_} :> {y, z}] //
First // ListPlot


Mathematica wants to use some kind of interpolation when making a contour plot, but there's no way to make a decent interpolating function for this. Without fixing your data (preferably at the source), the best you can do is to turn off interpolation altogether

ListContourPlot[data, InterpolationOrder -> 0,
ColorFunction -> "BlueGreenYellow", PlotLegends -> Automatic]