Remove blank spaces comm output

I have two lists of IDs that I am comparing with comm command. My problem is that output looks like this:

YAL002W
YAL003W
        YAL004W
        YAL005C
                YAL008W
        YAL011W

All I want to do is try to pipe it somehow so the file is written with out the empty spcaces, that translate into white cell when I open this files in excel. I have tried every possible combination I have found of grep, awk and sed to remove blank spaces without luck...
So I have came to the conclusion that columns are separated by one or two tabs respectively, therefore I can not remove them as easily as removing blank spaces without removing the formating of the file.

any help or suggestion will be welcomed. Thanks

EDIT:

I want my output to be three columns, tab delimited without the blank spaces

YAL002W YAL004W YAL008W
YAL003W YAL005C
        YAL011W

EDIT2 to avoit XY Problem as referenced:

Original problem (X): I have to lists and I want to find common and unique words between both lists (To generate a Venn diagram later on). So comm seemed like the perfect solution since I get all three lists at the same time, which I can later on import into excel easily.

Secondary problem (Y): The three columns that are generated are not three columns (or so I am starting to think) since I can't cut -f them, nor I can't remove the blank spaces with usual awk 'NF' or grep . (for example).

Given this input and comm output:

$ cat file1
YAL002W
YAL003W
YAL008W

$ cat file2
YAL004W
YAL005C
YAL008W
YAL011W

$ comm file1 file2
YAL002W
YAL003W
        YAL004W
        YAL005C
                YAL008W
        YAL011W

This will do what you asked for:

$ cat tst.awk
BEGIN { FS=OFS="\t" }
{
    colNr = NF
    rowNr = ++rowNrs[colNr]
    val[rowNr,colNr] = $NF
    numCols = (colNr > numCols ? colNr : numCols)
    numRows = (rowNr > numRows ? rowNr : numRows)
}
END {
    for (rowNr=1; rowNr<=numRows; rowNr++) {
        for (colNr=1; colNr<=numCols; colNr++) {
            printf "%s%s", val[rowNr,colNr], (colNr<numCols ? OFS : ORS)
        }
    }
}

.

$ comm file1 file2 | awk -f tst.awk
YAL002W YAL004W YAL008W
YAL003W YAL005C
        YAL011W

but of course you could just skip the call to comm and use awk right off the bat:

$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR==FNR {
    file1[$0]
    next
}
{
    if ($0 in file1) {
        colNr = 3
        delete file1[$0]
    }
    else {
        colNr = 2
    }
    rowNr = ++rowNrs[colNr]
    val[rowNr,colNr] = $0
}
END {
    for (v in file1) {
        colNr = 1
        rowNr = ++rowNrs[colNr]
        val[rowNr,colNr] = v
    }

    numRows = (rowNrs[1] > rowNrs[2] ? rowNrs[1] : rowNrs[2])
    numRows = (numRows   > rowNrs[3] ? numRows   : rowNrs[3])
    numCols = 3
    for (rowNr=1; rowNr<=numRows; rowNr++) {
        for (colNr=1; colNr<=numCols; colNr++) {
            printf "%s%s", val[rowNr,colNr], (colNr<numCols ? OFS : ORS)
        }
    }
}

.

$ awk -f tst.awk file1 file2
YAL002W YAL004W YAL008W
YAL003W YAL005C
        YAL011W