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I'm using grouping column in highcharts, I need to show only usage columns in tooltip(shared: true). But I see all grouping column http://jsfiddle.net/8o6umxdp/, I want to see only the values of the columns in this field, not grouped. I'm hiding this legend "showInLegend: false" but this legend is showing in the tooltip.

Highcharts.chart('container', 
 chart: 
 type: 'column'
 ,
 title: 
 text: 'Monthly Average Rainfall'
 ,
 subtitle: 
 text: 'Source: WorldClimate.com'
 ,
 xAxis: 
 categories: [
 'Jan',
 'Feb',
 'Mar',
 'Apr',
 'May',
 'Jun',
 'Jul',
 'Aug',
 'Sep',
 'Oct',
 'Nov',
 'Dec'
 ],
 crosshair: true
 ,
 yAxis: 
 min: 0,
 title: 
 text: 'Rainfall (mm)'
 
 ,
 tooltip: 
 headerFormat: '<span style="font-size:10px">point.key</span><table>',
 pointFormat: '<tr><td style="color:series.color;padding:0">series.name: </td>' +
 '<td style="padding:0"><b>point.y:.1f mm</b></td></tr>',
 footerFormat: '</table>',
 shared: true,
 useHTML: true
 ,
 plotOptions: 
 column: 
 pointPadding: 0.2,
 borderWidth: 0,
 grouping: true
 
 ,
 series: [ 
 name: 'Tokyo',
 data: [0, 0, 0, 0, 0, 0, 5, 0, 0, 0, 0, 0],
 grouping: 'tok',
 showInLegend: false

 , 
 name: 'Tokyo',
 data: [1, 0, 3, 0, 4, 0, 0, 0, 0, 0, 0, 0]

 , 
 name: 'New York',
 data: [0, 0, 0, 0, 33, 0, 0, 0, 0, 0, 0, 0],
 grouping: 'mew',
 showInLegend: false
 , 
 name: 'New York',
 data: [80, 0, 0, 42, 23, 0, 0, 0, 0, 0, 0, 0],

 , 
 name: 'London',
 data: [48.9, 38.8, 39.3, 41.4, 47.0, 48.3, 59.0, 59.6, 52.4, 65.2, 59.3, 51.2]

 , 
 name: 'Berlin',
 data: [42.4, 33.2, 34.5, 39.7, 52.6, 75.5, 57.4, 60.4, 47.6, 39.1, 46.8, 51.1]

 ]
);

but here only berlin and london, how to hide tokyo and new york

You could replace your pointFormat with a pointFormatter and filter by Series.showInLegend.

For example (JSFiddle):

// ...
tooltip: 
 pointFormatter: function() 
 if(this.series.options.showInLegend !== false)
 return '<tr><td style="color:'+this.series.color+';padding:0">'+this.series.name+': </td><td style="padding:0"><b>'+this.y.toFixed(1)+' mm</b></td></tr>';
 

This should mimic your pointFormat style, but allow for more dynamic inclusion.