Most of the perfboard layout you can find on Internet are some 2D top view design made with specific software just like VeroCAD or DIY Layout Creator. I tried that kind of software but didn't really liked it. I'm using the Proteus Suite really often and I wondered if I can use it to design my perf. In fact it's pretty easy if you know how to use the 3D Visualizer of ARES (depending of your license maybe ou can't use it).
Step 1: Draw the Circuit Board on ARES
Here I want to design a standard 5*7cm (2*2.75" ) perf which is a 24 colums (A to X) 18 rows (01 to 18) pads board with a space between them of 2.54mm (0.1"). First I put all the 432 pads (circles of 80th) using the 2.54mm grid. Next I draw the board edge and the rows/colums label on top and bottom (don't forget to do a X-axis mirror for the bottom silk text).This board has some square zone on top so i finished by drawing them.
Now you must save your layout. Select all the card you drawed and then select "Make package" (check you just have the board edge , pads and text before. No copper should be here)
Step 2: Let's Check the 3D New Board
Now your model (or something really like) must appears on your 3D view window. By default the card is green with tin pads and yellow top silk. I choosed to make it a little bit more real by using the same colors than my model.
Step 3: Adding Components
Now we can add some composents to our board. Enter the package library, select the one that you need and drag it to the perf layout (you can use the ISIS components library to check the name of the package you need ). In most of the time when you drag a components on board Proteus notice you that you did some errors (DRC errors) but here we don't care. You can (if you want to) draw the link between the components using a thick bottom silk line (will look like a copper track on 3D window)