This first answer is different from my second. This answer relates to what the OP tried to accomplish, while the second solves the main problem that the OP tried to overcome.
Gnuplot will not be able to do this on its own, since the corresponding styles (boxes and histograms) work only in 2D. You will need to do this with an external program.
For example, using your data and your 2d command (your first command), we get (using your data and the associated values ββ-100 and 4 for binstart and binwidth)

To draw these squares on a 3d grid, we will need to use the line style and have four dots for each: lower left, upper left, upper right and lower right. We can use the previous command and capture it in the table, but this will only give the top center point. However, we can use an external program for preprocessing. The following python makehist.py program does just that.
from sys import argv import re from math import floor pat = re.compile("\s+") fname = argv[1] binstart = float(argv[2]) binwidth = float(argv[3]) data = [tuple(map(float,pat.split(x.strip()))) for x in open(fname,"r").readlines()[1:]] counts = {} for x in data: bn = binwidth*(floor((x[-1]-binstart)/binwidth)+0.5)+binstart if not bn in counts: counts[bn] = 0 counts[bn]+=1 for x in sorted(counts.keys()): count = counts[x] print(x-binwidth/2,0) print(x-binwidth/2,count) print(x+binwidth/2,count) print(x+binwidth/2,0) print(max(counts.keys())+binwidth/2,0) print(min(counts.keys())-binwidth/2,0)
Essentially, this program performs the same function as the smooth frequency option, but instead of getting the top center of each window, we get the four previously mentioned points along with two points to draw a line along the bottom of all the boxes.
By running the following command
plot "< makehist.py data.txt -100 4" u 1:2 with lines
produces

which is very similar to the original graph. We can use this in 3D graphics.
splot "< makehist.py data.txt -100 4" u (1):1:2 with lines
which produces

This is not all so beautiful, but puts the histogram on a 3D plot. The same method can be used to add multiple data files to it. For example, with additional data
Index Angle 0 85.0804 1 92.2482 2 90.0384 3 99.2974 4 87.729 5 94.6049 6 86.703 7 97.9413
We can use
splot "< makehist.py data.txt -100 4" u (1):1:2 with lines, \ "< makehist.py data2.txt -100 4" u (2):1:2 with lines
for creating
